


Pretty When You Cry

by sublime42



Category: Doctor Who (2005), Torchwood
Genre: Crying, Cutting, F/M, Flashbacks, Hurt/Comfort, Implied/Referenced Rape/Non-con, Mpreg, Post-Traumatic Stress Disorder - PTSD, Rape, Self-Harm, Sickfic, The Doctor (Doctor Who) Whump
Language: English
Status: In-Progress
Published: 2020-01-05
Updated: 2020-08-15
Packaged: 2021-02-27 08:27:26
Rating: Mature
Warnings: Rape/Non-Con
Chapters: 22
Words: 23,709
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/22134037
Author URL: https://archiveofourown.org/users/sublime42/pseuds/sublime42
Summary: Missy tricks the Doctor and sexually assaults him for days. Clara helps to pick up the pieces.(Please read the tags)
Comments: 26
Kudos: 65





	1. Chapter 1

He'd been so incredibly stupid, he thought to himself in hindsight. Stupid to think that Missy had really changed for the better. Though, to be fair, she had put _a lot_ into it. Contacting him, apologizing so many times, crying, even.

He had forgiven her quickly, but worse, he had let his guard down. He hadn't expected what happened next. 

Through all their battles, there had never been any sexual components. Yet within minutes he was disarmed of his sonic and handcuffed to a bed. His legs were also tied so that he was lying spread eagle.

With a vicious glimmer in her eye, Missy set out to truly dominate him.

00

It took him nearly three days to get away. In the end, he pretended to enjoy it. Enjoy _her_. It killed him inside to do it, but there was no other option. He moaned in feigned ecstasy when she slid down on him, begged to kiss her and touch her. Told her how he wished he had experienced this sooner. It was his first time in this body, after all.

And somehow, she bought it, enough to let him out of his restraints at least. 

He had been so grateful to get back to the TARDIS, but as it faded away, he began to feel sick. The reality of what had happened began to hit him.

00

Clara was in the middle of a relaxing day of catching up on her favorite shows when the TARDIS appeared, breaking her coat hanger as it landed.

She rolled her eyes. Why couldn't the Doctor avoid breaking her things?

She waited for the doors to open for several minutes, but when they didn't, she grew concerned. She stood up and made her way towards the door, carefully pulling it open. 

"Doctor?" She called out. 

There was no response, so she stepped inside. 

"Doctor, where are you?" She walked towards the console and continued to look around.

It was the sound of a whimper that caught her attention. She turned towards the stairway to see the Doctor sitting with his back to his bookshelf, a blanket wrapped around him. He looked to be naked, and his knees where pulled to his chest. He was shaking.

Quickly Clara ran up the steps. Something was obviously wrong. 

"Doctor?" She kneeled down, as to be at his eye level. "What's going on?" 

She reached out to touch him but he pulled away, shaking his head. She noticed tears hitting the floor and realized he was also crying. It scared her, really. This incarnation of the Doctor never showed such emotion. 

"Hey, okay. I won't touch you," Clara whispered. "But clearly something happened. Can you tell me?"

A sob hitched in the Doctor's throat and he pulled the blanket tighter around himself. He hadn't had time to grab his clothes from the floor of Missy's room before his escape. The TARDIS had provided the blanket to him.

"Missy," he finally answered. 

"Did she hurt you? Where are your clothes?" 

He shook his head again. 

"Left them," he finally muttered. 

Clara sighed.

"Please let me take you to the med bay at least. We can make sure you're alright physically."

The Doctor sniffled. 

"You'll stay?" He asked softly.

"Of course," Clara answered. "Of course I'll stay."


	2. Chapter 2

The Doctor and Clara moved slowly towards the med bay. The Doctor could walk, but he felt extremely sore. Missy had her way with him in more than one position. She had used toys on him. The dried blood on his thighs told him that something must have torn.

The thought crossed his mind that perhaps Clara should not be there for this. As much as he wanted her protection, was it worth the disgust she would surely feel towards him? He could be strong enough to do it alone. 

He stopped Clara as she reached for the doorknob. 

"I changed my mind," he told her, though he couldn't meet her gaze. "I can do it myself."

Clara stared at him, surprised. 

"I'm sure you _can_ but I'm not sure that you should. You know I want to help you, Doctor."

He sniffled again.

"You... you'll think differently of me," he whispered. "And I can't bear to lose you over it." 

"I would never leave you over something like this. I want to help you," she repeated. "I swear I won't think less of you."

She was looking at him, eyes wide. It felt like she was being honest. God, he hoped she was.

He finally nodded and motioned for her to come in.

00

He had needed Clara's help to get onto the bed. Every movement made him feel worse. As he sat on the side of it he noticed Clara eyeing his legs. The blood was visible. She looked horrified but kept quiet.

Gently she pulled a blanket over his hips.

"Use the scanner." He pointed at a small cylindrical object attached to a wire.

Clara held it up and watched as the Gallifreyan symbols on it reformed into English. She pressed the start button and aimed it at the Doctor's head, then slowly moved it across his body.

The scanner beeped when it was done, and a monitor next to the bed lit up. The Doctor saw the read out first, his skin going pale as he read it.

"What is it?" Clara asked. 

The Doctor shook his head.

"Nothing I won't heal from," he answered. 

"Can I look?"

The Doctor considered for a moment. 

"I promise you, I won't think any differently of you."

The Doctor sighed.

"Yes you will. You won't have a choice. Go ahead, look. Someone else should know anyway."

Clara wasn't sure what to make of that. She moved to his side and looked at the screen. Her jaw dropped as she read it.

"Internal bruising... rectal tearing... My God, Doctor. She raped you!"

The knowledge made her feel sick. She swallowed and took a deep breath, gasping as she felt the Doctor squeeze her arm. He was crying, again. Quietly. His eyes were red and his hand shaking as he gripped her.

"I'll need help. With the...the treatment. But I'll heal fast," he said. 

"Of course. Anything you need. Do you want to clean up, first?"

The Doctor nodded. Perhaps a bath would help take some of the filth he felt on himself away.

00

The Doctor sat in the bathtub in the dark. Turning off the lights made him feel safer for some reason. He had asked Clara to get him a set of clothes, which he had placed on top of the toilet lid. She had chosen a pair of very soft pajamas and socks. He was grateful for it. The thought of having to put on one of his suits again bothered him. Missy had paid such particular attention to his garments, slowly removing them from his body, and using his jacket to wipe up bodily fluids.

The thought made bile rise in his throat. It burned as he swallowed it back, causing him to choke. As he sputtered there came a knock at the door.

"Doctor? Are you alright?"

Clara. She was standing guard outside just as he had requested. 

"Fine," he gasped out. 

It was then that he realized how hot the water was. It was near scalding. How hadnt he noticed it? He moved to turn off the faucet but pulled back as the metal burned his hand. The feeling took him back to Missy. She had used candle wax on him at one point, no doubt trying to be seductive, but the warmth of it had burned him. Being at a much lower temperature, it wasnt that hard to burn a time lord.

He was brought from his thoughts by the lights coming on. Clara rushed over and turned off the water then looked him over.

He was rocking back and forth, still breathing loudly and heavily. 

"Doctor. Doctor, listen to me," she said, getting on her knees next to the tub. "Your skin is red. I think you burned yourself. I'm going to help you out of the bath, okay?"

She didn't trust him to stand on his own. Well, maybe that was good. Because he began to doubt whether he actually could.

He said nothing as she drained the water. 

"Probably easiest if you put your arms around my neck and I will pull you up," she said. 

The Doctor nodded and put his shaky arms around her. She wrapped her arms around his chest and stood him up, allowing him to lean against her as she grabbed a towel. 

"Is it okay if I wrap this around you?" She asked.

After he nodded in agreement she quickly and efficiently she tied it around his waist. 

"Can you dry yourself off?"

The Doctor shrugged. For some reason he felt incredibly weak.

"Can I do it then?"

"Yes," he whispered. He leaned against her as she worked, forcing her to take much of his weight. It soon became clear to her that he needed to sit lest he fall over.

She moved his clothes from the toilet and sat him on top of the lid, then poured a glass of water and handed it off to him.

"Drink that," she instructed. 

It scared her how he instantly did as he was told, forcing himself to drink the entire thing. As he finished she noticed his hands shaking again, so she took the glass away.

"You need to sleep, Doctor. You're exhausted and in shock. I'll help you get dressed and get to bed, but first you need to begin treatment." 

His body tensed up as he considered this. 

"I have the antibiotics ready for you. And the suppository." She passed him the pills first, then refilled the glass with more water. The medical scan had noted that he was suffering from dehydration and low blood sugar among his other injuries, so more water was good for him.

He carefully placed the pills on his tongue and attempted to bring the glass to his lips, but his hands were shaking too hard. Clara wordlessly helped him, one hand on the glass and one gently rubbing his back as he drank.

"Do you think you can put in the suppository?" She asked. She hoped he could. Having her do it would probably make things worse for him mentally. 

He nodded 'yes', and Clara turned her back, allowing him some privacy. 

He dropped the towel and carefully inserted the medicine, unable to stop himself from groaning in pain as it touched the cuts inside of him. It contained a numbing agent, but it took a few seconds to kick in. 

"Itll hurt less soon," Clara reassured him. "Do you want to put your pajamas on before I turn around?"

The Doctor didn't respond but she could hear him pick the clothes up.

Somehow, he managed to get them up, but he needed help with the drawstrings. 

"I'm just going to tie this, alright?" She said.

"Yes."

"Do you need help with the shirt?"

The question made him break down again. Had Missy destroyed him _that_ much? Made him so weak that even his hands barely worked?

Hearing him sob broke Clara's heart.

"Why don't you leave it off for now?" She offered, handing him a tissue.

He took it and blew his nose, and attempted to wipe his tears away.

"Come to bed." She took his hand and led him out of the room.

00

He didn't want to go to his own room. He made that clear by shaking his head vigorously when they approached it. He strongly preferred Clara's room.

Thankfully Clara didn't mind. She could easily sleep on the floor. It was more important for the Doctor to rest than it was for her to do so.

She pulled back the covers of her bed and watched as the Doctor crawled in. She noticed that there were marks on his chest- bite marks and what looked like cuts from where a whip or belt had hit him. His ribs were sticking out, too. Even though he had only been gone for three days, he had somehow lost weight.

That reminded her: she still had one more thing for him.

"Doctor, before you go to sleep, try to eat this." She pulled out a wrapped item from her pocket. It was small and smelled like coconuts and chocolate. It looked like chocolate, too.

"The TARDIS listed it as something you should have. It provides all your nutrients or something."

He took the bar from her and nodded. It was a very quick way to regain necessary calories and nutrients. Usually it was given to famine or shipwreck victims who hadn't had food for days.

He unwrapped it and slowly bit into it. Clara smiled at him, as if silently telling him that he was doing a good job.

They sat quietly together as he finished it. He took his time, afraid that eating too fast might make him sick. The food contained an anti emetic but it wasn't all that strong.

When he was finally done, Clara took the wrapper from him.

"I was thinking I'd sleep on the floor, if that's okay?" She asked.

The Doctor frowned. He didn't like the thought of her being uncomfortable in her own room. But he knew he needed to rest, and sleeping on the floor would prevent that. He briefly considered asking her to stay, to sleep next to him, but he decided against it. It was bad enough that she had to care for him in this disgusting state. It was unfair to force her to sleep next to him, too.


	3. Chapter 3

The night was long. Clara barely slept, having woken up every hour or so to the sounds of the Doctor having nightmares. 

The first three times she woke him, and he seemed somewhat relieved to find that he had only been dreaming. But after the fourth one, he had woken up hard. He had dreamed of Missy. She was sucking him off, her hand going up and down with her mouth, and though he tried to fight it he couldn't help but keep an erection. 

Clara had seen it. He knew she did. She didn't say anything, but he knew, and it broke him. The tears came again. She rubbed his back, tried to shush him, but the knowledge that she knew just how dirty he was hurt deeply. 

For her part, Clara was nervous. She didn't want to touch the Doctor too much but she wanted to help him stop crying. Rubbing his back wasn't helping. And then the sobs turned into coughs, which turned into retches, and soon the Doctor and the bedspread were covered in vomit. It was a mix of water, bile and bits of half digested chocolate from the nutrient bar he had eaten. It was all over his face and ran down his heaving chest.

Unsure of what else to do, she ran to the med bay hoping to find something to help clean him up. While there she noticed the monitor flashing again. It was almost as if it were trying to get her attention. 

She walked over to it only to see a preloaded injection needle roll into a pan used to hold the medication the TARDIS distributed. 

Clara sighed. She didn't like it, but she probably ought to use it.

00

The Doctor had thrown up again by the time she returned. And he still seemed hysterical. He was frantically clawing at his arms, scratching deep enough to bleed in some places.

This wouldn't do. She had to act.

"Doctor!" She put her hands on his shoulders. 

The action stunned him for a second and he looked at her.

"Doctor, you're having a panic attack, or a flash back or something. The TARDIS gave me this," she held up the needle. "It'll help you calm down. Can I give it to you?"

She didn't know if Missy had drugged him, and giving it to him against his will seemed wrong. 

"Please," she said, when he didn't answer, "You need to calm down. You're hurting yourself." 

The Doctor swallowed nervously, but nodded 'yes'. The only thing keeping him grounded in any way was her hands on his shoulders, but he knew that it wouldn't last long. 

Clara stuck him in his thigh. The medicine quickly took effect.

00

The medicine calmed the Doctor down and made him drowsy. Even though he was half asleep, Clara took pains to tell him everything she did before she did it.

She removed the bedspread and used towels and warm water to clean the doctor's chest and face. He whimpered as she ran the towel down his chest, his eyes fluttering open with a look of fear. 

"I'm only cleaning you off, I promise," Clara told him.

He simply closed his eyes in response. 

She considered removing his pajamas, but they were still fairly clean and she thought doing so might traumatize him more, so she left them on. He barely moved when she cleaned and bandaged the cuts on his arms.

Finally, she placed another blanket on top of him. It was soft and warm and covered with pictures of constellations. She had brought it from home. He snuggled into it as he felt it. 

The medicine was supposed to last ten to twelve hours. She hoped he would be able to sleep for most of it. 

She was about to move back to her spot on the floor when he reached out to her, grabbing her hand. 

"Please... stay..." he whispered. 

"Are you sure?" She felt like she had to ask. He was medicated, after all. 

"Please. Was scared to ask before."

Clara nodded. Fair enough. 

She crawled into the bed next to him. Almost instantly, he turned towards her, rested his head on her chest and wrapped an arm around her waist.

00

The next morning, the Doctor wouldn't get out of bed.

At first Clara thought it had to do with the medication, but by the afternoon it should have worn off. Plus, he seemed like he was awake, but pretending to be asleep. 

She wasn't sure what to do. Every time she tried to shake him awake his eyes would flutter open and he would pull the covers back over his head in attempt to hide.

By the early evening she was really getting nervous. He had to take his medicine and he needed something in his system. 

She tried to tempt him with foods that he liked. Pancakes, for instance, were a favorite, but he refused. She tried soup, toast and cookies before a last ditch attempt with another nutrient bar.

"Please, Doctor. You need to eat and drink. I know you have superior biology but even you can't go this long without sustenance. If you won't do it for yourself than do it for me."

She held his hand as she spoke. Finally, his eyes opened. He forced himself to sit, grimacing in pain as he did so. He was mostly healed, but still sore. The lack of nutrients was making the process take longer.

He didn't understand why she was being so insistent. He was dirty, now. Tainted. Destined to burden her. But she sounded so upset! So, he decided to obey.

Clara unwrapped the bar and handed it over to him, only to see him shove the whole thing in his mouth. He stared at the wall while he tried to chew it, but it was tough and chewy and he was having a hard time. It kind of reminded him of the gag that Missy had forced him to wear. And with that thought, he felt sick again. This time Clara saw it coming. She placed a napkin in front of his mouth. 

"Spit it out," she ordered, as if she were talking to a young child. 

The Doctor did as he was told, looking at her sadly. He hated that he couldn't even follow her instructions correctly. 

Clara threw the napkin away and left the room, returning a minute later with a banana. 

"Let's try this again." 

She sat next to him on the bed, peeled the banana and broke off a piece of it. She handed it to him and watched him eat it.

It was easier for him to chew and swallow. He did his best to clear his mind and focus only on Clara. She kept giving him bits until the whole thing was gone.

"Good job," she praised, smiling at him.

It made him both happy and sad. Happy that he had done what she wanted, but sad that he had sunk so slow as to be praised for something as simple as eating.

00

Clara got him to take his meds and drink a glass of juice. It had a nutrient powder mixed in, in an attempt to restore some of what he needed.

As a reward, Clara put on a movie. She sat up against the bedframe, inviting him to snuggle up to her if he wanted to. Only if he wanted to.

Despite his feelings of unworthiness, he moved closer, resting his head on her lap. Clara pulled a blanket over him and stroked his hair until he fell back asleep.


	4. Chapter 4

The more Clara thought about it, the more she understood Missy's actions. They were horrible, but effective. What better way to get the Doctor out of her hair than by crippling him mentally.

It made her angry. Beyond that, really. Rage was more like it. She would make the bitch pay in time, but for now she tried to focus on helping the Doctor. 

Physically, he was almost totally healed, but mentally he was still suffering. 

What scared Clara most was how clingy he had become. It was as if some switch turned in his mind, making him feel that he needed her protection but also didn't deserve it. He would beg her to stay with him for hours just lying in bed. She obliged, but noticed that after he asked her he had started scratching himself again, reopening his cuts.

She had to take extra care to reassure him that she didn't mind being there, that she wanted to stay with him, but after days of this it was getting difficult not to snap.

Ultimately, she felt that a very short break to leave the TARDIS and get some clean clothes from her room was in order. It would give her ten minutes on her own, to breathe a little.

And it had felt great. She instantly felt relief as she left. Ten whole minutes where she didn't have him right behind her. Then she returned and found him sitting on the console floor, rocking back and forth and staring at the door, waiting for her, clearly panicking that she might not return. 

She forced herself not to react negatively and helped him to his feet, then led him back to her room.

00

The Doctor knew that he was frustrating Clara. He could tell by her body language, even if she said otherwise. He didn't want it to be this way, but the fear in his mind only quieted when she was nearby.

It was wrong. All of it was wrong. He was supposed to protect her, not the other way around, but everything he did reminded him of Missy. Still, eventually she would leave if this kept up. 

There had to be something he could do to fix this for both of them. Perhaps the TARDIS could provide a medication to help numb him. 

He lost his train of thought as Clara spoke up. He'd been hiding out in her room for most of the day, ever since she had come back from her trip to her closet. It was the only place where he felt remotely calm.

"Doctor, I think it's time you take a shower." She told him. It was the only way to get him to do such things - she had to tell him to do it. If left to his own devices he would lie in her bed forever.

He looked at her, his eyes pleading what he felt too nervous to say.

"I'll stay with you," she assured him. 

He mumbled a thank you and carefully stood up. Though he was almost entirely healed, he still felt sore. Probably because he had gone from being very active to very sedentary. His body wasn't used to lying around all day. It wasn't just depression keeping him down though - he felt tired constantly and could think of nothing to explain it.

She followed him to the bathroom.

"Do you need to go?" She asked. Usually she waited outside when he used the facilities. 

He nodded yes and slowly walked in.

"I'll be out here. Call when you're done."

00

Clara was thinking about what to do next when she heard a cry. It wasn't too loud, but it definitely sounded pained. She knocked on the door.

"Are you alright?"

When there was no response, she tried again.

"If you don't answer me I'm coming in," she warned.

She sighed. Silence again. Usually that meant he was either crying, or too afraid or upset to talk.

She pushed the door open only to find him leaning against the sink, clad only in boxers. His trousers were still around his ankles.

"What's going on?" she asked, confused.

"There was blood," he whispered. 

Well, she hadn't expected that. She supposed it made sense though. He'd only recently been eating enough to allow for regular use of the bathroom, and his insides had been torn up pretty badly. 

"It's okay," she told him. "You're not still bleeding, right?"

He shook his head 'no'. He hated that he had to tell her about this. His old self would've just suffered in silence. 

"We can do another scan just to be sure, but it's probably left over from before you healed."

He nodded again and allowed her to lead him towards the bathtub. Gently, she helped him undress, telling him what she was doing the whole time - it seemed to keep him calm when she did that. Once he was naked, she turned on the shower to a moderately warm temperature. 

"Don't change it," she warned him. Three times so far she had found him standing in scalding hot water. It was part of the reason she stayed with him when he bathed now. He always told her that he didn't remember changing it, but she wasn't so sure it was the truth.

00

After he finished, she helped him dress in a new set of pajamas along with a pair of slippers, and led him out to the med bay. She knew the area well by now, having been there so many times to gather medicine and bandages for his cuts.

"Sit down," she instructed. 

He sat on the bed perfectly still, his hands cross in his lap, watching as she readied the scanner. She aimed it at his chest and worked her way down. The results popped up a few second later.

"No new cuts. You're all healed. But there's a suggestion to draw blood for tests," she said. 

He was looking at the screen, reading it as well. There was something going on - the TARDIS was concerned about something, but wasn't telling him what.

He wasn't even sure how to react to that. How much worse could it get? Did Missy give him some kind of disease? He wasn't sure if he cared if she did.

"Want to do it now or later?" Clara asked.

The Doctor shrugged. Might as well do it now.

Clara nodded and readied a needle, following the TARDIS' instructions for blood drawing. The Doctor didn't even flinch as she did this.

The sound of pills hitting the medication pan came as Clara placed a bandage on the injection site. 

"These are benzos," she said, reading off the description provided. "Time Lord friendly anti-anxiety meds."

"Okay." So the TARDIS had heard his request.

"You want to try them?"

"Yes." It couldn't make things any worse, could it?

Clara wordlessly gathered the medication and placed it into a container, then helped him off the bed. Despite being so stoic while she drew his blood, he held onto her tightly as they walked. It reminded her of helping her gran cross the street in a way. 

She settled him back into bed and handed him the remote. He'd been working his way through a bunch of Earth programs lately. Mostly mid to late 90's sitcoms, weirdly.

Once he was comfortable, she handed him a bottle of water and two of the pills.

"The instructions said to take two every twelve hours," she explained. 

"Okay." He put them in his mouth and swallowed them down.

00

The medicine worked quickly. Within an hour, he felt calmer. His hearts, which seemed to be going much faster lately, had slowed their paces. He still felt guilt and fear in the back of his mind, but it was easier to tune out.

Clara noticed that his expression had changed. He looked panicked and dejected earlier. Now he just looked relaxed. He didn't protest when she brought him lunch - sometimes she had to demand that he eat, or he would go far too long without food. The fact that he ate everything surprised her, but in a good way. She didn't want to get her hopes up, but so far, the meds seemed like a good thing.


	5. Chapter 5

The Doctor slept calmly throughout the night. Only two nightmares, no panic attacks. Clara had slept next to him, and he held her, but he didn't keep her awake with twitching like he often did. 

They got up a bit earlier than usual - he didn't need to sleep later since he wasn't waking up constantly - and she brought him breakfast in bed along with two more pills, which he took with no objection. He looked better. More rested. He even sat up a little straighter. 

"Do you want to take a walk in the gardens today?" She asked. The TARDIS had a huge garden area, and he desperately needed some time outside of the bedroom.

He surprised her by answering yes. 

She didn't push it by making him wear his suit. Rather, she allowed him to wear his pajamas and slippers. When they stepped outside, he closed his eyes and turned his face towards the light, sighing as he felt a warm breeze blow across his skin.

They walked for a while before he began to get tired again, and then they sat under a tree. Despite feeling calmer, he still preferred to be near her, and she wasn't all that surprised when he rested his head on her shoulder. She wrapped her arm around him and pulled him closer. 

The pair sat silently, and Clara wondered if perhaps he had fallen asleep again when he spoke up.

"Clara, before Danny, were you with many others?"

Clara blinked. She hadn't expected that question.

"You mean in a relationship with others?"

The Doctor shrugged.

"Sexually?" She tried again.

He nodded 'yes'.

"Well, a few. Not...not that many, but I was with other men before him."

This had to do with what had happened with Missy, she reasoned. 

"What about you, Doctor? You've... been around the block a few times, I take it?"

"Not in this body. Or the last one," he answered. "Not until..." he trailed off. 

She felt a wetness on her shirt that meant he was crying again, quietly this time. 

"I know it's not much, but I promise you, Doctor, I will make her pay for what she's done."

She held him tighter as she spoke and it seemed to relax him slightly.

She didn't know what she would do, but she would find a way to make sure that Missy regretted ever touching him.

00

The rest of the day went better than she expected. After they went back inside, the Doctor calmed down. He had no issues eating, taking his medicine or bathing and he even spent a few minutes on the console room.

The blood test that the TARDIS had requested had slipped Clara's mind until late in the evening. She was about to fall asleep when she recalled it. Carefully, she untangled herself from the Doctor, tucking him in again to make sure he didn't get cold as he slept.

Quietly she walked to the med bay, where she found the monitor blinking with information. The message nearly made her fall over. Plus - he was a male - it wasn't possible, was it? Time Lord biology couldn't be _that_ different, could it? She ought to do a re-test. Maybe send the sample to a lab on Earth, see what came back then.

She wondered if she should tell the Doctor about it or not. If it was a false positive - which it had to be, really - it would just upset him. Better to get more information first.


	6. Chapter 6

**Summary for the Chapter:**

> The poor Doctor finds out some rough news.  
> (Please read updated tags)

A month had passed since the Doctor had returned. He was still taking his medication, and doing generally better. He'd been able to talk to Clara a little more about what had happened, and he was able to sleep in his own room at least part of the time. All in all, he seemed to be healing, at least a little bit.

The only issue was that blood test. She'd ran it through the TARDIS one last time before calling in a favor. Her ex worked at one of the NHS blood labs, and could use the equipment to perform a test. She explained that it was her own blood, not wanting to raise any major red flags.

When he completed the test he called her back.

"This is not your blood," he said. "If it is, you've got something seriously wrong with you, because I've never seen any results like it."

"Maybe it got contaminated?" She offered. 

"Maybe. But I doubt it."

Clara was silent for a moment.

"Were you able to perform the test I asked for?"

"Well, yes. Congratulations, you're pregnant. And you really, really ought to go in for a checkup."

Clara tried not to seem too surprised.

"Right. Thanks. I will. Don't tell anyone about this, yeah?"

"I won't."

Clara smiled. 

"Thank you. I owe you big time."

00

Clara wasn't sure how to tell him. He was finally doing okay. Eating right, sleeping normally. He'd even offered to take them on a short trip somewhere. This knowledge would set him back tremendously. But he had to know. He'd figure it out on his own eventually.

She had decided to wait until the weekend to say anything. Let him have a good week, she thought to herself. They took a trip see a local constellation and had a picnic lunch in the garden, and all seemed well until Friday.

That day, the Doctor woke up, jumped out of bed and ran straight for the bathroom. Clara followed him, concerned that something was wrong, and found him vomiting. He was covered in sweat and shaking, barely able to hold himself on his knees. She came behind him and rested a hand on his back, trying to comfort him.

It took nearly half an hour for it to stop. When it finally did he collapsed on the floor panting and dizzy.

She pulled him so that his head was resting on her lap and petted his arm, telling him that he was okay and that she was there to help. 

She finally got him back to bed after another fifteen minutes. 

"Something's wrong," he said once he had calmed down. "Something's different."

Clara frowned. 

"There is something you need to know." She took his hand, noticing that he tensed up at her words.

He stared at her. 

"What? Did Missy give me some disease?"

"Not quite. Oh...I'm not sure how to say this. It's going to hurt you."

"Just say it," he told her.

"You're... well, somehow you're pregnant, Doctor."

00

The Doctor blinked.

"You're kidding," he replied. "This is no time for jokes, Clara."

"You have no idea how much I wish I was joking. I ran the test twice, had my friend test it at the NHS labs. You're pregnant. About five weeks along, I guess."

The Doctor didn't answer, but he gripped her hand harder and began to shake. 

Clara jumped onto the bed and wrapped her arms around him, pulling him into a hug.

"I know this is scary and unexpected, but you're not alone," she reminded him.

The Doctor didn't respond. He looked to be focusing on breathing, taking deep breaths in and out. 

"Is it... is it normal for male Time Lords to become pregnant?"

Slowly he shook his head no.

"It's not normal. Usually no sex is required for procreation, we loom children. I've only heard of it happening one or two times, and both were Time Lords who lived isolated existences, usually with one or two other Time Lords or Ladies around. It's like on a genetic level, their bodies felt there was a threat to the population, and their bodies would change and allow for the healthiest person to carry a child. Which makes sense why it happened to me, now that I'm saying it out loud."

He looked pale, but a bit calmer.

"I can't imagine how you must feel," Clara admitted. "If... If you prefer not to keep it, maybe we can find a hospital, somewhere? There has to be someplace we can go."

The Doctor nodded.

"I have to think about it."

00

The Doctor asked to be alone after that. Clara was wary of it, but felt she had no choice but to leave him be. She quietly asked the TARDIS to alert her if he needed anything and made her way to the library, hoping to find books on Time Lord physiology.

The one she found a section on male pregnancies under a tab labeled 'rare conditions'. It outlined the cases of the men that the Doctor had mentioned, and how they had both carried their babies for a full term (ten months, as opposed to human's nine, due to the baby's need for a more highly developed brain) and had delivered healthy children. 

The men listed were younger than the Doctor, at least in the bodies that they had when they carried the children, by at least thirty years. They both looked to be young, healthy men. She wondered if the Doctor's current age would impact him in any way. She couldn't well imagine a human woman his age carrying a child.

The symptoms list seemed similar to what a human woman might go through during a pregnancy: nausea, weight gain, mood swings, cravings and dizziness, but it noted that pregnant Time Lords required much more sleep than usual and might feel soreness throughout their body as their physiology adjusted.

Well, that explained why the Doctor was so tired all the time. 

Clara bookmarked the page and closed the book. She'd been in the library for over an hour and was wondering if she ought to go check on the Doctor. As if on cue, lights in the hallway outside the library began to flash. She got up and followed the corridor to the bathroom.

00

He had to keep it, right? He and Missy were literally the last of their species. Who knew when he could get Gallifrey out of the time lock. It could be centuries. And a Time Lord child would provide a companion who would not die like all the others.

But, it was Missy's child. He hadn't a choice in its conception. How would he be able to look at the baby, knowing it was the product of assault?

But that wasn't the child's fault. The baby had no say in any of this either.

He rocked back and forth, leaning up against the wall, his fingers steadily scratching away at his arm. There was a lot of blood, now. He didn't care. The scratches had been open deeper, bigger, and took up much of his forearm. It was the only thing allowing him to remain sane right then. the pain of it kept him grounded.

Even if he wanted this child, could he safely carry it? Maybe in one of his last three incarnations, but now? Now he was older. He already felt the effects of it on a daily basis before all of this. Back and knee pains. He couldn't eat certain foods lest he get sick. It was nothing terrible, but enough to be a daily reminder of his age.

The sound of the door opening pulled him from his thoughts. Clara stood beside him, eyes wide, a look of worry on her face.


	7. Chapter 7

The time after that seemed like a blur. He remembered her washing his arm, cleaning it and bandaging it, then taking him back to her room where she sat him down.

After several minutes of silence, he spoke up.

"The medication I took," he started, eyes watering, "it might impact the baby."

"It's possible," Clara replied.

"And I'm old, Clara. I don't know if I could handle this." He gestured to his abdomen. 

"I understand," Clara said. 

"So... So maybe, it's best to not... not go through with this."

He felt numb, now. Like he was on autopilot. Some rational part of his brain had kicked into gear and was doing the thinking for him.

"Alright. We'll find a place to help you, then."

The Doctor nodded.

"Thank you."

00

The place they found was a hospital ship floating outside of Therilia V, created three hundred years in the future. The Doctor had asked Clara to call ahead and notify them of his arrival, too afraid to make the call himself. He wasn't sure he could get the words out if he tried.

The Therilians were humanoid looking, but with a bluish skin tone. All of them had bright green eyes and either blonde or purple hair.

As they exited the TARDIS, two of the nurses greeted them. They were young and pretty but wore solemn expressions, knowing that what he was about to do was not something to be taken lightly.

The Doctor gripped onto Clara's arm as they followed the nurses. He felt sick already. Not from morning sickness, just in general. But this had to be done. He couldn't handle carrying it. He couldn't handle any of this. Even before he knew about the pregnancy, he was just barely hanging on.

They were led to a room that was painted an awful green color, perhaps meant to be comforting in some way but missing the mark completely. It reminded the Doctor of all the times he'd been sick while waiting for this appointment.

After getting the Doctor situated on a bed, one nurse moved to take his vitals while the other held a tablet.

"The last information we have on you was from your last...er, self," the nurse with the tablet stated. "We have to update it, to make sure we can keep you safe during the procedure."

The Doctor nodded in agreement, remaining quiet while the first nurse used a small instrument to measure his pulses.

When that was done, the second nurse held up her tablet, using it to scan the Doctor's body. It reminded Clara of the scanner on the TARDIS.

"Ah, yes, I can see the fetus here," she noted. "Looks to be around six weeks along. The procedure should be simple, then. We'll use a very small, precise laser to destroy its body, and the remains will be re-absorbed by your body. The changes you've been undergoing should reverse in a few weeks. 

"Alright," the Doctor agreed. 

"We'll have to sedate you, of course."

The Doctor nodded. It was taking all of his willpower to remain strong during this. Inside his mind he was screaming, wanting to thrash around and hit things due to the stress of this.

"And your wife, here, will take you home?" The nurse asked, looking at Clara.

The fact that the Doctor simply agreed put up red flags in Clara's mind. He never would allow someone to refer to her as his wife! They weren't even in a relationship!

"Doctor," Clara said, resting a hand on his, "If you want to reconsider this, we can always come back later."

The Doctor swallowed nervously.

"No, no. We're here now."

Hearing this, the nurse held out the tablet.

"Please sign your consent," she said.

The Doctor scribbled something on the tablet using his finger and handed it back.

"We'll begin shortly," the nurse told him, picking out a hospital gown from a bin, "First, put this on."

00

The first thing the Therilian doctor did was give the Doctor a pill designed to calm him. He began explaining what he was doing after that kicked in, narrating how he would attach an IV for the sedative and how the procedure would take less than five minutes.

The Doctor listened, closing his eyes as he felt the needle inserted into his arm. The medication blocked out much of his fear and stress, allowing him to focus on things like his heartbeats. 

He felt the anesthesia hit his vein, it burned as it entered, and suddenly, his focus changed. He wasn't listening to his heartbeats anymore - he was listening to someone else's. He looked up to see the face of a little girl standing before him, with dark brown hair and eyes like his own. She couldn't have been more than five or six. She smiled at him and hugged him.

It was his child. Or future child. How could he harm something that sweet and innocent?! It went against everything that he stood for!

"Stop!" He called out. "Stop now!"

But the anesthesia had already begun to take effect.

00

The Doctor woke up twenty minutes later. He felt woozy and sick, but mostly worried.

"You did it?" He asked the doctor. "Is it over?"

"No, sir. You started shouting at me not to do it, so I didn't proceed. We let the anesthesia wear off. You're still pregnant."

"Thank Rassilon," the Doctor muttered. 

A second later, he was overtaken by a wave of nausea.

Clara helped the Doctor back to the TARDIS, moving slowly as he still felt sick. She led him back to her room and tucked him until bed.

"I'm going to get you some food. Do you need anything else?" She offered.

"No, but we'll have to go to the med bay later, see about vitamins and such."

He had a small smile on his face and was resting a hand on his stomach. Clara wasn't sure what to make of it. The look of happiness on his face seemed too good to be true.


	8. Chapter 8

**Notes for the Chapter:**

> TW for self harm. Please see updated tags.

Things seemed to be calm for the next month. It surprised Clara. She had expected far more angst. 

So far he hadn't had many rough symptoms, either. He was sick some mornings, but not always, and was tired a lot, but otherwise seemed alright.

He'd started taking short walks around the TARDIS garden, then having a nap under the tree when he felt sleepy.

Today she had walked in on him while he was getting dressed. He was shirtless, and looking at himself in the mirror. He still looked mostly the same, though his stomach stuck out just the smallest bit. No one would notice it if they weren't looking, they would just think that he had started eating more regular meals. The Doctor seemed quite in awe of it though.

"You're starting to show," Clara noted.

The Doctor sighed and started putting on his shirt.

"It's odd, seeing her there." 

"Her?"

"I think it's a her," he whispered. He was quiet for a moment, lost in thought. 

"I wonder who she will look like," he added.

After that, his mood changed. He skipped his walk, preferring to stay in Clara's room, watching the television.

00

The thought about his child's appearance brought everything back. He had been pushing it away for weeks, but he realized that every time he looked at his child, he would always be reminded of Missy .

He also hated how his body was changing. It wasn't just his stomach that looked different. He could feel his body slowly adjusting and creating a birth canal for the baby to use. His hormone levels were rising and he felt sore constantly.

It was emasculating. He knew he should be past feelings like that- his species was so advanced in regards to gender constructs- but he still felt it and it bothered him. Not only was he old, but weak too. Too weak to get away from Missy and now he was paying for it.

He had to stop taking his medicine weeks ago. Thankfully, it hadn't done any damage so far, but the possibility of it happening in the future existed. And so he had to deal with these feelings on his own.

What to do, what to do, he wondered. Instinctively he began to scratch at his arm but he caught himself before going too far. Clara would see it if he hurt himself there. 

Then another thought popped into his mind: she didnt regularly see him naked, not recently at least. Maybe there were other areas of his body that he could take out his frustrations on. He healed quickly, anyway, and it wouldn't harm the baby. It was win-win.

He felt much calmer now that he had a plan. The bathroom was the safest place to do it. He could lock himself in, clean up and Clara would never know. She didn't even look up from her book when he got up to leave.

00

Minutes later he had pulled down his pants and was running a diamond tipped razor across his upper thigh. The relief was instant. Almost euphoric. He couldn't help but focus on anything but the pain of it.

Three long cuts. That's what he allowed himself. When he was done he disinfected them and bandaged his leg, feeling much more clear headed than previously. He took care to destroy the remnants of his actions, flushing the bloody tissues away and cleaning the floor of stray drops of blood. 

As he walked back to Clara he felt the cuts pressing against his pants, throbbing dully. 

"Everything okay?" Clara asked when he returned. 

"All good," he smiled at her.

She smiled back and returned to reading.


	9. Chapter 9

Soon Clara finally felt confident enough to consider going back to her old life, at least a little bit. She and the Doctor had been spending their time in the vortex and she wanted to see her friends, family and colleagues again. 

The Doctor seemed to be doing well. He was eating regularly, sleeping a lot and only rarely had panic attacks during the day lately. The nightmares still happened, but she could always return to stay with him in the evenings. 

With all that in mind, she was quite surprised by how he reacted when she mentioned it. 

"You want to leave?" He asked, his face paling. She could see him start to breathe harder and he gripped onto the console exceptionally hard.

"Not permanently!" She tried to assure him. "Just during the day for a bit. I'd like to go back to work, see my class and friends. I'd come back at night."

The Doctor tried to hear her. He could understand what she was saying but his mind kept interpreting it differently. 

When he didn't respond, Clara got worried. He looked like he might be sick or collapse or something. She quickly went to him.

"I'm going to hug you," she told him.

He nodded, just barely, but seemed to calm slightly when he felt her arms around him. She felt him lean down to rest his head on her shoulder before she heard a very quiet sob.

"Ohh, Doctor! Come sit with me."

He didnt respond but he followed her as she guided him to the steps. They sat next to each other and Clara wrapped her arms around him again, this time rubbing his back. He was still shaking, doing his best to stay silent.

She let him cry. Better for him to get it out. She moved her hand from his back to his hair and began to play with it.

"I know it might be scary for you to be alone. Perhaps this is too much too soon. Why dont we compromise. You come with me when I leave. We will stick to places like my flat and only visit people you've met before."

The Doctor considered this.

"Alright," he finally agreed. He didn't like it, the TARDIS was his safe place, but he knew that if he didnt allow Clara some time away she would eventually leave permanently.

00

The next morning, they planned to have breakfast at the local cafe.

"We'll start small and see how you feel after that." Clara had explained. 

But he wasn't even out of the TARDIS yet and already he was feeling nervous. 

He had been sick that morning, worse than usual, and it had taken him over an hour to recover. His stomach still hurt, but he imagined it was more from nerves than anything else at that point. To top it off, his legs were bothering him as well. He had been running low on space there lately and had literally reopened some old wounds. They throbbed whenever he stood.

But Clara had looked so excited, he couldn't ask to put their trip off. 

She came up behind him and took his hand. Instantly he relaxed slightly. 

"It's going to be fine," she reassured him. "I'll be with you the whole time."

00

The walk to the cafe was fairly uneventful but the Doctor was still on his guard. His stomach continued to ache, but he kept quiet.

Thankfully it was a Tuesday morning and after the morning rush, so the place wasn't too crowded. Clara led him to a table and they both sat down.

While she read over the menu, the Doctor looked around. This wasn't so bad. 

Then a waitress came by to drop off food at the table next to them. She was middle aged, with dark hair, light eyes and stern features. She wasn't Missy, but she reminded the Doctor of her. His hearts began to beat faster and his mouth went dry. His chest started to burn as bile rose in his throat. This was not going to end well.

Seeing the Doctor cover his mouth, Clara pointed at the restroom and watched as he practically ran to it. When he returned ten minutes later, he was sweaty and shaking. 

She quietly apologized to the staff and walked him back to the TARDIS.

00

The cafe incident set the Doctor back. Once again he was clinging to Clara constantly, literally following her from room to room. If she so much as used the bathroom, she had to talk to him while he waited outside the door. He seemed to be terrified that she would disappear and that if this occurred, Missy would return.

She wasn't sure what to do. Assurances only helped for a brief time. He would go to sleep knowing that she would protect him but wake up afraid again. 

It was grating on her again, if she was honest with herself. She wasn't going to leave him, but there was only so much she could take. And really, she missed her old friend. He used to be so brave and logical while the man...or alien, rather...sleeping in her bed wouldn't sleep unless she was holding him.

He had an appointment on Therilian in two weeks, and she resolved to talk to the doctor about getting him some help.


	10. Chapter 10

He hadn't thought about the hospital gown. How hadn't he thought of that? He always thought of everything! He wondered if this pregnancy was making him dumber. Or perhaps his preoccupation with constantly being in fear had made him forget. He hadn't been feeling too great lately either, so he supposed that didn't help things. 

But anyway, the gown presented a problem: while he was mostly healed, several light cuts remained on his legs. Two had gotten slight infections and had thus taken longer to heal and he had several newer ones on his calves. 

There had to be something he could do. Cancel the appointment, perhaps? Or just keep the TARDIS in the vortex longer until all the cuts were gone. But Clara was there and she would wonder why they were waiting. She had been especially pushy about this appointment, too. Kept saying how they needed to talk to the doctor about medication or therapy. Kept looking him over and saying he looked sick, too, and that it worried her.

In the end, he supposed that he could rely on doctor-patient confidentiality. It might hurt Clara to be asked to leave the room after he changed, but it was his right, and with a little luck he could get through this without any major issues.

00

Healer Arlox had treated hundreds of pregnant patients but the Doctor was the most interesting one he had ever had. He had never met a Time Lord before and their physiology intrigued him. As such, he took very detailed notes on the Doctor.

But when the man first arrived, he could immediately tell that something was wrong. The Doctor was limping, pale and sweating. 

The Therilian was very concerned, especially when the Doctor requested to be examined alone.

His wife seemed surprised by the request, but agreed to leave, stating only that she needed to speak to the healer afterward. 

Once the Doctor was gowned up, Arlox understood the Doctor's request. But how to proceed with the exam? Clearly, the Doctor was not of sound mind. His cuts were obviously self inflicted. But Arlox didn't want to startle him and risk him running off.

"You won't mind if Healer Archady joins me while I review the scan, will you?" Arlox asked. Archady was one of his oldest friends and most trusted colleagues. He would be able to help restrain the patient if necessary. 

"That's fine," the Doctor answered. He just wanted to get this done with.

Arlox smiled and called for Healer Archady to assist him, giving him the code word for 'potential issue with patient'.

Once the second healer entered, Arlox began the scan, shaking his head as he looked over the results. 

"What's wrong?" The Doctor asked. "Is something wrong with her?"

"Doctor, you have a high fever," Arlox noted. "The scan is showing a severe infection on your left thigh. It's gone to your bone. This is extremely serious."

"Oh, that? That's...not a worry. I have medicine I've been taking for it."

"Clearly it isn't working," Arlox replied.

"What about the baby?"

"The baby is fine for now. But if your infection progresses it could shut down the systems keeping her alive. You are right that she is a girl, by the way. It looks like you've lost weight since you were last here, too."

"Well I've been sick every morning. I'm not sure how you expect me to gain any," the Doctor replied. 

"I understand, but you're losing too much so we need to treat your sickness so you can eat. With this and the infection I could admit you, but with the cuts as well...I am sorry, Doctor, but I think we need to admit you for a few days."

The Doctor sat up. 

"Absolutely not." 

Being admitted would mean being without Clara and his ship. He would be defenseless. There was no way he could do it. His hearts would probably give out from the stress of it.

"Doctor, let us cut to the chase. Those wounds are self inflicted. Anyone can see that. You need help and we can help you."

The Doctor started shaking.

"I can't! You don't understand! I can't be away from her! And I'm not safe here! Anyone can get me. _She_ can get to me!"

"She? Listen, Doctor, we don't have a choice. I can't rightfully let you leave in this condition." Arlox glanced at Archady, who had already moved to the Doctor's side. The Doctor flinched when touched. 

"We can start with a week and reevaluate after that. Now, are you going to make this difficult or easy?"

00

It took the two healers nearly an hour to catch the Doctor. If he hadn't been so weak, they wouldn't have caught him at all. They'd found him in a supply closet, hiding in a corner and barely conscious.

He didn't have the strength to fight them by that point. They simply strapped him into a wheelchair, applied some wrist and ankle restraints and wheeled him out.

Clara was waiting in the room that they took him too, looking more anxious than he had ever seen her. Healer Archady began maneuvering the Doctor onto a bed while Arlox explained what was happening. 

"Do we have your approval to proceed?" Arlox asked. He was still under the impression that Clara was the Doctor's wife. 

Clara looked at the Doctor sadly. He truly did look awful and this place could do much more for him than she could. 

"No, please," he whispered to her.

Clara's eyes filled with tears.

"I'm so sorry Doctor but I think you need to stay. I'll visit you every day though, I swear." She reached for his hand and squeezed it.

He began to cry too, and Clara felt her heart break.


	11. Chapter 11

The Doctor woke early the next morning unsure of where he was. He remembered feeling very sick, and being worried about something, and going to the healers, but that was it.

He was lying on a bed in a room with light blue colored walls and an image of Therilian's purple sky projected onto the ceiling. 

The hospital. He was at the hospital. But why?

His back hurt, so he tried to move over, but found that he couldn't. His hands were tied down. So were his ankles. This set off alarm bells in his mind. Closer inspection revealed that he was dressed in a gown. Why was he tied down? Where was Clara?

"Clara?" He called out, hoping that she was nearby and had a good explanation for this. "Clara? Where are you?"

There were footsteps, but they were too heavy to be coming from her. Healer Arlox appeared.

"Doctor, you're awake," he said, smiling. "How are you feeling?"

"Why am I tied up? What's going on? Where's Clara?" He was getting frantic. She wouldn't just leave him like this. Had something happened to her? 

"Doctor, please try to take a deep breath so I can go over everything with you. You're safe, Clara is safe, everything is alright, I promise," the healer told him.

The Doctor could sense that the man was telling the truth, so he tried to do as he was told. He took a deep breath and held it, then let it out slowly.

"Good, good," Arlox said, continuing to smile. "Your memory is probably a little hazy. We had to give you a lot of medication. You're very sick, Doctor. You have a severe infection and a high fever, and you kept panicking... it was best to sedate you, let you rest, and give you the antibiotics you need."

It was then that the Doctor noticed the IV lines plugged into his arm.

"Those are to provide the medication, along with hydration and nutrition. Your wife was helpful in regards to looking up information on your ship related to your biology."

"Where is she? Where's Clara?" 

"She will visit you later today after your therapy. We have you scheduled to meet with one of our best psychologists."

"Pfft," the Doctor rolled his eyes, "what's the point? They won't be able to help."

"At the very least, Doctor, they'll be able to listen," Arlox answered.

00

The Doctor did his best to act calm, but his stomach hurt. The longer he waited, the worse it got. He was sure it was nerves. He usually didn't have an issue talking to new people-well, the old him didn't - but the prospect of speaking to this therapist person scared him.

He was almost sure that he might be sick when the door to his room opened. In walked a small female Therilian. She had large eyes not unlike Clara's and had a similar tiny frame. It made the Doctor feel slightly more comfortable. 

"Good morning! I am Healer Narang. I believe Healer Arlox told you I was coming."

The Doctor nodded. 

"I'm here to talk with you and see if we can help with some of the issues you've been experiencing."

The Doctor frowned.

"I don't want to discuss it."

"It?" Narang pulled up a chair next to his bed. 

"The incident which led to my predicament."

Narang flipped through her papers.

"Your pregnancy, you mean. I can only take that to mean that you were assaulted. Of course it would be a very painful topic for you."

"It is," the Doctor replied.

"We don't have to talk about it right now. Why don't we start out with what you're currently feeling. And while you're talking, why don't you hold onto this?" She produced a small box from her pocket. She undid his wrist restraints and handed it to him.

He took it and examined it.

"A Therilian puzzle box?"

"Yes. You can either try to solve it while you talk or press on the buttons. They have different textures that patients sometimes find reassuring."

The doctor immediately set to work on the box. He was silent in concentration for a few moments. Therilian puzzle boxes were known for their complexity. 

"So, Doctor, what are you feeling?" Narang asked again.

"Stressed. Tired. Sick," he listed off, not once looking at her.

"I can imagine. Are you stressed because you're here?"

The Doctor shrugged.

"Perhaps you're worried about someone. Your baby? Or your wife?"

The Doctor sighed and began to press one of the buttons with his thumb. 

"Clara," he whispered. 

"Are you worried something has happened to her?"

The Doctor glared at the healer.

"Don't even joke. I'm afraid she..." he trailed off.

"Go on," Narang encouraged. "I won't judge you. And it might feel better to get it out."

"I'm afraid she won't come back," he said, under his breath. Just the statement made him want to cry. He pressed harder into the box, willing the tears to stay back.

"I see. Why do you think she might not return?"

The Doctor sniffled, still doing his best to remain strong. 

"I don't want to discuss this," he tried again. 

"But we have to. The only way you can leave is if you are healthier. So tell me, why do you think Clara will not come back?"

"Because I'm beneath her! Because she doesn't need...need any of this," he stammered, throwing the puzzle box at the wall. "Because she's better off without me! I'm just holding her back. Who wants to be with someone who...who can't even get coffee without panicking? Who has to be locked up? Don't you understand? If she's any smart she would run away and never come back."

He was shaking, now. His hand moved to his arm and he began picking at his skin. Tears ran down his face and he was beginning to feel as if he couldn't breathe. His chest felt too tight. His oxygen bypass would kick in soon. He started to feel dizzy.

"You're alright, Doctor," Narang told him. She was by his side now. "I'm going to take your hand, okay?"

He didn't verbally respond but did his best to move his hand so that she could easily reach it. As soon as she touched him, he felt more at ease. A wave of calm swept over him and within a moment his breathing began to slow. 

"Psychic energy transfer," he whispered. "You're doing this. Making me calm."

"Yes. I am projecting a calm feeling to you. I was afraid you might get sick. Just breathe for a few moments. Inhale for five counts, hold for five, release for five."

The Doctor closed his eyes and did as instructed, focusing on counting with each breath. Gradually he felt the energy flow taper off, but he still felt much calmer. 

"There," Narang said, smiling at him. "You're doing so well. As much as I'd like to continue our discussion, I think you need to rest. I'll be by tomorrow to talk some more. For homework I want you to think of reasons why Clara has stayed with you thus far. Good reasons and bad reasons. You can say them and the board in front of you will list them." She pointed at a white board that hung on the wall. 

"Okay," he replied.

He didn't move as she returned his restraints. He was too tired now. Maybe if he went to sleep, Clara would be there when he woke up.


	12. Chapter 12

Pity.

The word appeared on the white board. He had said it out loud.

That was probably the biggest reason she stayed. She pitied him. Felt bad for the old man who clearly couldn't fend for himself anymore. 

The word grew darker and larger as he pondered it; the board picking up on his emotions.

She was too good, too kind to let him go. The thought hurt, and he felt nearly sick again. She wouldn't have pitied him in his last body.

In fact none of this would have happened if he were still that young. He would have been able to fight Missy off. She might have even considered him not worth the risk. His current age had made him an easy target. 

What else? Guilt, perhaps? The word appeared beneath the first.

She had mentioned a few times, before all of this, that she had felt bad about what had happened after Danny died. That she felt like she still owed him for his forgiveness. Maybe that had to do with it? She was paying back his kindness?

The word darkened slightly but still remained small. Pity seemed more likely.

The sound of the door opening pulled him from his thoughts.

For a second he felt panicked but he quickly relaxed when he saw Clara. Only then did he realize that there were tears on his face, his dark thoughts having hurt him _that_ much. He wished he could wipe them away.

"You came back," he whispered. 

"Of course I did!" She forced a smile. "I wouldn't just leave you. They only let me see you now."

The Doctor stared at her, but didn't respond. He still felt slightly stunned that she was actually there.

"I brought you something," she continued, holding up the small bag that he had only just noticed. "It's banana ice cream. The TARDIS suggested it, and the healers said you can have it."

"Thank you?" He half questioned. "But I'm... I can't quite eat right now," he said, moving his arms to draw attention to his restraints. 

Clara nodded.

"Well, I can help if you'll let me."

"Alright," he agreed.

She sat on the edge of the bed, mindful of the straps keeping him in place and blankets covering him. Before opening the container she pulled a tissue from her bag and gently wiped his face, almost as if she had read his mind.

Then she opened the container, dipped in a spoon and held it to his lips.

The action made him feel like a baby or an invalid. He almost didn't want to eat it. But the look on her face, so kind and caring made him open his mouth. 

The treat was surprisingly good. He couldn't remember the last time he had eaten it. 

"It was in the freezer," Clara explained, as she fed him another bite. "Apparently things stay good in there for years?"

"Yes," he answered. 

She fed him again, her eyes never leaving his face. 

"I've missed you," she told him. "I keep getting up to look for you then realizing you're not there."

"I've missed you too. So much."

They continued in silence until he had finished half of the container. He couldn't eat as much as he used to. Clara simply closed it up and put it away.

It was then that she turned and saw the board.

"Pity and guilt," she read off. "What's this?"

"Nothing important." No need to have this discussion, he thought to himself. 

"It's on the wall of your hospital room in giant letters. It must be important."

He should have known she wouldn't drop it.

"Homework. From the therapist."

"And?"

"And... she asked me a question, and those are my answers."

"What was the question?"

The Doctor sighed. 

"It's really not important, Clara."

"Well, you don't have to tell me, but I'd like it if you did."

She was giving him that look, with her eyes all big and sad.

He frowned. How could he resist that?

"She asked me to list reasons why I think you might stay with me. Those are my reasons." He closed his eyes, not wanting to see her expression at his revelation.

There was another silence as she processed the information. Finally she spoke.

"You really believe this?"

Now he was starting to feel angry. This felt a little like picking at an open wound.

"Well why else would you? It's not as if we're going on adventures anymore. I can't give you anything. I can't take care of myself, never mind you, so what other reason is there besides pity or guilt?"

He was shaking again, his muscles tensing. This would be it. The thing that would make her leave for good. He was sure of it. He tried to brace himself for it.

But she didn't move.

"What about love?" She asked.

He opened his eyes. 

"Love?"

He wondered what was happening. Maybe he was hallucinating? Clara surely wouldn't be so cruel as to joke like this.

"I stay with you and help you because I love you, Doctor."

She looked sad now. Why was she sad? He hated his brain sometimes, emotions could be so difficult for him.

"Why sad?" Was the only thing he could get out of himself. 

"I guess I hoped that it was obvious. I don't pity you. I mean yeah, I hate what happened to you, but I'm not staying because of it. I care about you. I want to help you. I love you and you help those you love."

He loved her too. As a friend or more he wasn't sure. He wasn't sure what she meant by it either. But for now, just hearing it helped in some way. 

He felt her hand cup his cheek and he nuzzled into it, sighing again as her hand moved to his hair and she began to play with it. The feeling calmed him.

"You too," he said softly.

"I know."

Clara continued to comfort him, neither of them noticing that the sad, angry words on the board had disappeared.


	13. Chapter 13

"Love," Narang read off. 

The word had appeared the previous day, after Clara had left. It was big and neatly written.

The Doctor smiled.

"You look much better today. I heard you didn't fight the healers when they changed your bandages and you ate dinner and breakfast. It's a big change from just a day ago."

"As you said, I can't leave until I'm healthier," the Doctor replied.

Narang nodded. 

"So tell me what happened."

The Doctor related what Clara had said to him, the memory making him feel something. Something he hadn't felt in a very long time: hope.

"And knowing that she loves you has given you a reason to try," she concluded. 

"Yes."

"I'm very glad to hear this. Love is a wonderful thing that gives many hope. It will help you get through the darkest times. However, we still have to help you come to terms with what happened and what the future holds. Are you ready for that?"

The Doctor considered this for a moment. 

"I think so," he eventually answered.

00

While the Doctor continued his therapy, Clara was busy speaking to the healers. They had good news: the Doctor had started to heal, physically anyway, and assuming he continued to show a more positive outlook, he could be released within days. 

00

Narang held the Doctor's hand as he recounted his time with Missy. She sent a low wave of calming energy to him as he spoke, trying to prevent another panic attack. It seemed to be working. He managed to get through fifteen minutes of talking before his breathing picked up. Narang sent a stronger wave of energy and reminded him to focus on counting while breathing. The Doctor focused as best he could until the panic started to subside. He was safe here. Clara was nearby. Everything was okay.

When the session was finally over, his restraints were removed as a symbol of trust. If he could trust the healers and Clara to help him, they could trust him to not hurt himself. 

00

Clara was allowed to spend the night in the Doctor's room. She arrived wearing a set of pink pajamas, carrying a set of TARDIS blue ones for him along with more food and a book.

She had gotten permission to help the Doctor shower, something he was incredibly grateful for. He hadn't washed in days aside from the healers cleaning his wounds, and was feeling particularly gross. 

He took his time as Clara stood nearby. She smiled as he began to hum some vaguely familiar tune. That was something she hadn't realized that she missed: sometimes, when he didn't think she could hear, he would sing or hum to himself, sometimes as he played his guitar. She took the fact that she was hearing it again to be a good sign. 

He stepped out of the shower feeling much better but also tired. He was still fairly weak, and needed Clara's assistance to dry off and get dressed. Knowing that she helped him out of love and not out of guilt or pity made it slightly better at least. He felt less bad about relying on her. 

When they were done she led him back to the room and helped him into bed, this time crawling in to lay beside him, the same way they'd done on the TARDIS.

She picked her bag off the floor and handed him a container. 

"More food?" He asked.

"I figured you'd like it more than whatever they serve here."

He opened it to see chocolate chip pancakes.

"You made these?" He asked.

"Yes. And before you ask, they're cooked all the way through, and I made one for myself and ate it earlier and I'm not sick so I think they're fine."

He couldn't help but chuckle. 

"I appreciate you not poisoning me, Clara."

With his hands free the Doctor was able to feed himself, occasionally giving Clara little bites off his fork. She had done a surprisingly decent job. He assumed she had put a lot of effort into it, so he ate as much as he could. The look of joy on her face was worth any discomfort he might feel. 

When he was finished Clara cleaned up and took out the book she had bought. Closer inspection revealed it to be an electronic reader. 

"I thought maybe we could read together," she told him. "If you want, I mean."

"I want to. What story?" He fought the urge to sigh happily as Clara rested her head against his shoulder. He always felt so much better with her near him like this. 

"You choose."

He turned on the reader and began flipping through the titles downloaded onto it. He wanted something fun, or at least something that wasn't serious. 

"Here." He handed it off to her. 

She laughed as she read what he had selected.

"The Princess Bride? Really?"

"It's a good story!" He smiled at her.

"It is. I just didn't expect it. Want me to start, then?"

"Mhmm." He moved closer to her and pulled a blanket over both of them. 

"Alright. Here goes." Clara turned to chapter one and began to read. 


	14. Chapter 14

**Notes for the Chapter:**

> The next chapters after this are much longer.

The Doctor had nightmares that evening. He dreamed of Clara disappearing and not being able to find her. He dreamed of going into labor by himself, with no one to help, and of Missy coming back and taking the child while he was even weaker than before, and therefore unable to fight her off at all. It was the feeling of something touching his face that woke him. He opened his eyes to see Clara looking at him, concerned. Healer Arlox stood in the doorway. 

"I was doing my rounds just now," he explained, walking over to the wall where a board monitored the Doctor's vitals. His hearts were racing, but slowly the beats were decreasing in speed.

The Doctor barely heard him. He still felt terrified. Clara being there helped, and kept him tethered, so to speak, but he was one step away from pure panic.

"Didn't the therapist give you an exercise?" Clara asked. "Counting breaths?"

The Doctor nodded in agreement.

"Why don't we do it together," Clara suggested.

She inhaled and tapped her hand against the Doctor's arm five times, held her breath and did the same, then exhaled and counted once more. He followed her lead, his hand tightly gripping her thigh. 

It took a few minutes for him to calm. By then he felt exhausted again. The healer was still there.

"Doctor, we have medications that can help you sleep," he began. "Herbal remedies, they wouldn't harm your baby if used correctly."

The Doctor was too tired to process what the healer was saying. He simply replied with "okay" and sunk back into Clara's arms as soon as the healer left.

00

Five days later, the Doctor was released. His cuts had healed, his infection was cleared, and he had gained enough weight to be considered healthy. The conditions of his release were that he continue to attend therapy with Healer Narang once per week, and that he attend checkups every two weeks, or sooner if he required it. Clara agreed to help hold him to his promise.

His issues weren't nearly gone, but the relaxation techniques that Narang had taught him, and the sleep medication that Arlox had provided were at least making him somewhat capable of functioning. 

His first night back on the TARDIS was spent in Clara's room, cuddled up in her bed, sharing chocolate cake for dinner with her and watching Friends until they fell asleep.


	15. Chapter 15

Over the next four months, the Doctor continued to attend his therapy sessions, and slowly he began to feel more like himself. He felt secure enough to regain a small amount of independence - now he slept in his own room three nights each week, and he no longer required Clara to be next to him constantly. It still felt nice when she was, but he didn't panic if she was in another room.

Physically he had changed as well. His stomach definitely stuck out now, though it was probably more noticeable because of his lanky frame. It made him self conscious, especially because his chest was softer too. He knew he wouldn't actually grow breasts as a woman would, but the amount of female hormones surging through his body made everything more rounded. Even his hips were slightly wider. On the bright side, his wrinkles had also softened. Overall he had a somewhat more androgynous appearance.

The fact that Clara seemed to like it stunned him. At the very least, she complimented him more. He wasn't sure if she was doing it to boost his ego, or if she really meant it, but he did his best to assume that she was telling the truth.

Their relationship was... well, he wasn't sure how to define it. They trusted each other implicitly, telling each other their deepest, darkest fears. She had seen him at his absolute worst, and so he felt he could be open with her. In return, she began to open up more to him, telling him about some of the harder things she'd dealt with in the past. Things that somehow he'd missed in his research of her.

Over time, he found himself feeling attracted to her physically. It was odd to him, because he tended not to find anyone particularly attractive, but something about her began to captivate him. Every few days he found something new that he enjoyed, whether it was the freckles that showed at night when she removed her makeup or the softness and scent of her hair.

But that was where it ended. The few times that he'd become aroused thinking of her had made him feel sick with guilt and nerves, the feeling taking him back to what had happened with Missy, and how dirty it had been, how she'd used him. That was literally the only thing he didn't tell her about, if only because he wasn't sure how to explain it without making her feel incredibly uncomfortable. If he did fantasize, he did his best to focus on smaller things, like holding her hand, or sometimes, kissing. He'd never kissed someone in this body. Not willingly, at least. The idea of a gentle kiss from Clara was one of the few things that he truly enjoyed.

00

That day, they were off on an adventure. Well, not really an adventure. It was more of a day trip to a safe, highly civilized planet that he'd been to many times. He had friends there, and he'd contacted them ahead of time to make sure that they'd be around.

That was one of the things Narang had suggested: safety in numbers when in places that made him anxious, and most places outside of the TARDIS still made him nervous. 

Clara held his hand as they stepped out onto the pinkish soil of Kandira. The planet was largely rural, with small villages interspersed every few miles. The one they were currently in had a street market that he thought Clara might like, along with some very good restaurants.

"Doctor!" Someone called out.

The Doctor turned to see his friend Breon waving at him. Kandirans were humanoid looking, but had a third eye on their foreheads. 

The Doctor took a deep breath and mentally went over his story again. He'd have to explain his appearance, but telling the truth might put himself, the baby and Clara in danger. Missy was surely looking for him, and if word got out that the he was pregnant, it would be an even bigger issue. He'd rather take a hit to his ego then take the risk.

"Breon! How are you?" He asked.

"Doing well. And you look like you're doing well too, eh?" Breon joked, nudging him in the side. 

"Ah, my metabolism's finally slowed. Only took a few thousand years," he replied.

"Happens to the best of us," Breon answered. "And who is this?"

"Clara Oswald," Clara said, reaching out to shake his hand. "I'm the Doctor's friend."

"Friend, eh?" Breon nodded at the Doctor and Clara's hands. They were still clasped together.

"We're very close friends," she responded.

"Alright. Well, Mosie and Dax are waiting for us at the market. Ready to go?"

The Doctor nodded in agreement and he and Clara followed Breon into town.

00

It turned out that Breon, Mosie and Dax had helped the Doctor defend Kandira against an small army of cybermen. The three were all members of the town's guard, which made Clara understand why the Doctor seemed to feel safer around them.

The market was a lively one, with vendors selling various wares, from clothes to jewelry, food and ceramics. Clara stopped them at a stall that had clothing on display and pulled the Doctor in.

"This might be a good place to find you some new clothes," she said. 

"I don't need new clothes," he replied. 

"Umm, I'm not sure how to say this nicely, but yeah, you really do." 

She hadn't wanted to mention it, lest she hurt his feelings, but he hadn't been able to button his trousers in weeks, and the rubber band holding the two buttons together just looked silly. At least he wasn't wearing a waist coat anymore, preferring instead to wear looser, button down shirts, but even those were starting to get tight.

The look on the Doctor's face caught the attention of Mosie, the only other female in the group. He looked embarrassed.

"Aw, nothing to be upset about," she said, taking his other hand. She didn't notice how he cringed when she did so. "We'll find you some new outfits."

The two women began picking out sets of trousers and shirts, holding them up for the Doctor to see, while Breon and Dax poked around looking for clothing for themselves.

Once he'd accumulated several outfits, the stall owner led him to what looked like a large closet, telling him that he could try on his clothes inside. He was mildly amused to find that the closet was bigger on the inside, much like this TARDIS. It wasn't huge, but it was definitely several feet larger than it appeared.

In the end he chose two pairs of trousers with what felt like a stretchy material in the waist, and three new shirts that fit him much better. 

"Looking good, Doctor!" Dax said, as the Doctor walked out wearing one of the outfits he'd bought.

"Looking very good," Clara agreed. 

The Doctor nearly blushed at the compliment. 

Once again Clara took his hand and they began to walk.

00

Within a few hours the Doctor was very tired. This wasn't unusual. He required a lot of rest, especially as his pregnancy progressed. Still, he felt too embarrassed to ask for a break.

Thankfully Breon noticed how quiet his friend had gotten, and how slowly he was walking, and suggested that they stop somewhere for lunch. 

The place that was chosen was one that the Doctor was familiar with. The owner's sons had fought alongside them when the cybermen attacked, thankfully all had survived. 

"Doctor! So good to see you!" The owner, an older Kandirian man named Strile said. "And Breon, Dax and Mosie! What a wonderful surprise!" He hugged all of them then led them to a table.

"Order anything you want. It's on the house," Strile told them.

The Doctor knew what he wanted in a matter of seconds, ordering a large bowl of some kind of soup and a loaf of bread to go with it.

"Been craving that forever," he whispered to Clara.

She rolled her eyes.

"Tell me we came to this planet solely because you're craving Kandirian soup," she whispered back.

He smirked and shrugged.

Lunch was spent catching each other up on everything. Mosie was now a mother of two, and Dax had recently married his long term partner. Breon, forever a bachelor, was busy helping with his nieces and nephews. 

The soup that the Doctor had ordered was neon blue, and it had things moving in it. She wasn't sure if they were alive and she didn't really want to know. The smell of it was pretty horrendous, too. Yet he seemed to be eating it as fast as possible. She tried her best not to watch. Despite the grossness of it, it was nice to see him so happy, having such a good time talking with old friends.

00

They returned to the TARDIS that evening feeling exhausted. The Doctor quickly returned them to the vortex then made his way to his room, where he promptly took off his shoes and shirt. Clara followed behind, wanting to make sure he was okay. She found him lying on the bed, sweating.

"You okay?" She asked.

"So hot. And my feet hurt _so_ much."

She glanced down, noticing that his feet looked swollen. His shoes had left red marks on them.

"That looks painful," she noted. "Let me get you some water and maybe I'll consider rubbing your feet." She smiled at him.

He looked better when she returned. His hot flashes were usually quick, so she wasn't too surprised at that. He'd put on an old t-shirt that stretched across his belly and was leaning up against a large pile of pillows. 

"Here you go," she handed him the glass, watching as he chugged it down.

She sat on the edge of the bed and took one of the Doctor's feet into her lap.

"This okay?" She asked. 

"Mhmm," he sighed. 

She began to rub his foot, chuckling at the sounds of relief he made as she touched him. 

"We need to get you more comfortable shoes. Maybe a pair of flip flops," she said.

The Doctor didn't respond so Clara decided to tease him. 

"Or maybe a nice pair of Crocs. You'd look great in those. Maybe we can get them in TARDIS blue."

"Claraaa," he moaned. 

"Yes?"

"No Crocs. You know why Crocs have holes?"

"Why?"

"Because that's where your pride leaks out."

The two of them broke out laughing.

00

With the Doctor tucked into bed Clara had some time to herself. She used it to catch up on the research she was doing. She hadn't wanted to tell the Doctor, but the TARDIS had been alerting her to the fact that someone was scanning for them. The ship must have intentionally blocked the Doctor from seeing it, thinking how the anxiety of it might harm him, as he hadn't mentioned it and she imagined that if he had seen it, it would've been a big topic of conversation. For now, in the vortex, they couldn't be found. The risk only came when they landed.

Though the TARDIS could not definitively identify who was looking for them, Clara had a feeling who it was. She needed a plan and to think of a way to tell Doctor, too.


	16. Chapter 16

**Summary for the Chapter:**

> Jack and Ianto join the TARDIS crew.

**Notes for the Chapter:**

> I hated that Ianto died so I'm keeping him alive for this. I'm imagining it as after Children of Earth, Torchwood needs to be rebuilt, and assuming that Miracle Day has not happened yet.

Another month passed without event. The Doctor was really showing now, and his symptoms had gotten harder to deal with, for both him and Clara.

The worst was the mood swings and the cravings. They were both horrendous. At least before, if he cried, there was a reason for it. Now he might go from laughing to crying within minutes because they'd run out of his favorite ice cream.

That was his big thing now: ice cream. But not just normal ice cream. No, he covered it with the weirdest toppings. Ranch dressing, pickles and even raw alien calamari were all used at certain points. The space squid was the worse in her opinion, but she held back any rude comments. He seemed to be constantly eating now and that was better than him not eating at all, so she kept her mouth shut.

She was watching him finish off his third bowl of mint ice cream with the alien equivalent of apricot jelly when she noticed something hidden between some of the books that they'd left on the counter. "Oh!" She exclaimed, picking it up. "I'd forgotten this. I got it for you on Kandira." She handed the object over.

The Doctor examined it. It was a small blue and purple glass flower.

"The vendor said its supposed to bring good luck," she told him.

He said nothing, but reached into a container full of odds and ends that they kept. He pulled out an identical glass flower and handed it to her.

"I got the same one for you. I was going to give it to you on your birthday."

She looked at the flower, then back at the Doctor. He stared back at her, his hearts beating quickly. He had a nervous feeling in his stomach, but felt excited, too. He wondered if this was it - the time when they might finally kiss. His question was answered only a second later.

"Can I... can I kiss you?" She asked softly.

"Please," he whispered back.

Clara leaned in and gently kissed his lips. At first he seemed on edge but he quickly relaxed and did his best to kiss her back.

When they finally pulled apart, he took her hand.

"I love you, you know," he said.

Clara smiled at him.

"I love you too."

00

Their next trip was back to Earth, to Cardiff, of all places, where the Doctor had mentioned wanting to see another friend. Clara had heard him mention Jack Harkness before she had yet to meet him. She knew a little bit about him, though, and was hopeful that he might have some advice on what to do regarding Missy. 

She and the Doctor hadn't formalized their relationship, mostly because neither of them felt the need for it. They were happy when they were together, and things remained much the same as before, but with more kissing. While the Doctor had seemed nervous about it at first, once he got used to it he seemed to want to do it more often. He even started trying different techniques that he apparently had read about. Clara thought it was sweet, and it made her happy to see him slowly getting used to touch and intimacy, even if it was only something like kisses.

They landed inside a large building in Cardiff and stepped out into a dark room.

Clara was the first out of the TARDIS. She began looking around, trying to figure out exactly where she was. Then she saw a man approaching.

"Doctor?" The man called out. 

Upon closer inspection, Clara found him to be quite handsome, not that she would admit that out loud.

"Here!" The Doctor responded. He stepped out of the box to greet his old friend.

"You look different every time I see you," Jack noted.

"And you always look the same."

"Aren't you going to introduce me to this lovely lady?" Jack asked.

"This is Clara, and she is off-limits," The Doctor said, a possessive tone in his voice. 

Clara almost laughed, but she found him to be adorable, too.

"Alright," Jack put his hands up in surrender, "Off-limits. Got it. Hi Clara, I'm Jack Harkness." He reached to shake her hand.

She shook his hand and smiled at him.

"It's great to meet you. I've heard a lot about you."

"Good things, I hope?" He smiled back at her.

"Mostly!" She chuckled.

"I'll take it," he replied. "So what brings you guys here?"

"We've been visiting old friends and thought we'd stop by. It's been a while since we were on Earth," the Doctor answered.

Jack nodded.

"Alright, well, I'm always glad to see you. Should I give you a tour of the building? I've redecorated, as you can see."

00

The group wandered the building listening to Jack discuss what had happened to his team, and how they'd split up. He and Ianto were the only ones left, and Ianto was currently running errands. They walked for over an hour, after which the Doctor was feeling slightly tired. He was grateful when Jack offered them a place to sit.

"So, what else is going on?" Jack asked, as they got comfortable. He wasn't a stupid man, he could see that the Doctor was either sick or injured or something had happened.

The Doctor and Clara had previously discussed what they would tell Jack. The Doctor felt that he could trust Jack well enough to be truthful. 

"Well, I'm pregnant," the Doctor answered. 

"I see. Congratulations!" He grinned, "And you must be the...um, father? Mother?" Jack said to Clara.

The Doctor's face fell, and Jack knew he must have hit a nerve. The Doctor took hold of Clara's hand, his signal that he preferred her to do the talking.

"It's actually another Time Lord that's the other parent. You remember the Master?"

"How could I forget?" Jack sighed, "Such a horrible man."

"Well he regenerated and became the Mistress, but everyone calls her Missy. And Missy did some really terrible things to the Doctor, and now he's carrying her child." She decided to leave out the gory details.

Jack's jaw dropped.

"Seriously? That is awful!" He looked enraged, now. "Tell me she's dead."

The Doctor shook his head 'no'.

"Would you like her to be dead?" Jack asked. "I mean I know you're against murder and all, but... special circumstances..."

The Doctor glared at him.

"You've no idea how often I've wished it," he admitted. "But... I don't know that I could do it. She cut me deeply."

He looked ready to cry again, and Clara held his hand tighter. She and Jack were silent as the Doctor tried to reign in his emotions. When he finally seemed to calm down, Jack spoke again.

"You seem tired. Do you want to rest in my bunk for a little while? I can wake you up when Ianto returns," he offered.

The Doctor agreed and allowed Jack to show him to the bunk area. When he was sure that the Doctor was asleep, Jack made his way back to Clara. They'd definitely have to talk.


	17. Chapter 17

She's looking for us," was the first thing that Clara said when Jack returned. "I haven't told him, but the TARDIS keeps getting alerts about someone scanning for us. It has to be her."

"Does she know that he's pregnant?" 

"No. I mean, I don't think so. The only ones who know are you and his healers."

"So you think she's looking to hurt him again?"

"I think her goal was to break him and now that she's seen us moving around she knows that she didn't, so she's trying to finish the job." That was Clara's theory, anyway. 

"Eventually you'll have to face her," Jack said. "You guys just can't expect that she won't find you. You'll have to be ready for when she does."

"I know. That's why I wanted to talk to you. I don't think he can kill her. And honestly I don't know that he would forgive me if I did. There has to be another way to stop her."

"I'm sure we could think of something. She would need to basically be immobilized. Maybe put in stasis somewhere?"

"Something like that," Clara agreed. 

"Ianto and I can try to help you. Eventually we'll have to tell the Doctor about it though."

"I know we will. For now maybe you can travel with us for a bit? At the very least, having more protection on-board can't be a bad thing."

Jack considered her request.

"I'll have to talk to Ianto, but I don't think it'll be an issue."

00

The Doctor didn't seem overly willing to get out of bed when Ianto returned, so they let him sleep for a while longer. It was for the best, anyway, as Jack wanted to talk to Ianto alone about Clara's request.

Upon hearing of what had happened to the Doctor, Ianto quickly agreed to travel. The only thing left was to actually tell the Doctor that they wanted to join him. But how to do that without making the Doctor feel weak? Ultimately, they decided to play it off as a request for a break from the monotony of rebuilding Torchwood. Whether or not the Doctor saw through their lie, he welcomed their company aboard the TARDIS.

00

The ship set Jack and Ianto with a beautiful room not too far from the Doctor and Clara's rooms. It seemed as if she was in agreement that the Doctor could use all the help he could get.

Jack and Ianto had come up with a idea for a trap for Missy, should she become a threat again. It needed to be small and portable but also powerful, and they worked on it while the Doctor slept or was otherwise occupied. 

Things seemed to be going well, at least they thought so. A week in, however, reality came crashing down.

The Doctor was lying in bed, in his own room, this time, trying to sleep. The problem was that he could hear Jack and Ianto having fun together, so to speak, in their own room.

It wasn't overly loud. They were being polite, but he could make out the sounds of moaning and laughing and the sound of their bed moving.

At first he felt aroused by it. The thought of sex made him think of Clara, and of being intimate with her. He allowed the fantasy to begin, with hand holding and kissing, but as soon as he imagined anything else, flash backs of what happened with Missy came to him. Instantly, his arousal vanished and he began to feel sick.

He thought back to what Narang had taught him about panic attacks, and quickly began counting his breaths. When that didn't work he turned on the lights and started trying to distract himself by naming the objects around his room. 

When he finally calmed down, the depression began to set in. How could he ever really be in a relationship with Clara if he couldn't be intimate with her? She hadn't pushed him on it yet, but eventually she would want to be, it was only natural for humans. 

The thought kept him up for hours until he finally exhausted himself and fell asleep.


	18. Chapter 18

He was scheduled to see Narang in a day's time, so he decided to bring the issue up to her. In the meantime, he couldn't shake the idea that his time with Clara was limited.

Everyone had noticed a difference in his behavior. He seemed tired and irritable, snapping at Jack when he asked simple questions and not making eye contact with Clara. The latter action was mostly to keep himself from becoming upset if he looked at her too long. Deep inside, he had hoped that maybe they could truly be a couple. Maybe she would even help him raise his child. But now it seemed impossible.

Jack and Ianto kept out of his way, choosing to work on their project. Their idea was to make a small electrode that could stick on to Missy's clothing and spread to three points on her body. Once it was attached, one of them could hit a button and send a wave of electricity through it. It wouldn't kill her, but it would be enough to keep her stunned while they wired her up to a single-use vortex manipulator that would send her into a safe, unbreachable location before it self destructed.

It was harder to create than either had anticipated, so the extra time was useful. Clara, meanwhile, did her best to get to the root of the Doctor's bad mood. The harder she tried, the more he resisted, so she ended the day even more worried than before.

00

When the Doctor arrived at his appointment he was going on nearly two days of barely any sleep. He felt overly tired and frustrated and jumpy. Narang picked up on it quickly.

"What's happened since we last met?" 

"I was reminded of how things will never work out between Clara and I," he answered. 

"I see." 

Sensing this was going to be a difficult conversation, she handed him the puzzle box, which he immediately began to play with.

After letting him mess with it for a few minutes, she spoke again.

"So, why do you think things won't work out? Tell me the whole story."

The Doctor went into what had happened, how he'd been tempted to touch himself when he heard Jack and Ianto going at it, and how the image of Missy riding him as he laid tied to her bed popped into his mind.

"How can I expect her to stay in a sexless relationship?" He asked. He was crying now. He knew Narang wouldn't judge him.

"Well first off, there are many people who have survived sexual assaults who have gone on to have sexual relationships. It's not impossible. But it does take a lot of hard work on getting past the things that trigger you and learning to handle the feelings that come with them."

"I wish it hadn't been that way. Not the first time at least. I didn't even know what to expect and she forced all of it," he whispered. 

Narang handed him a tissue and watched as he attempted to clean himself up.

"It's not fair, I agree," Narang said. "No one should have to go through what you did. But I'm here to help you get through it."

00

The therapy session had left the Doctor exhausted. He went back to the TARDIS and fell asleep in Clara's room for the rest of the afternoon. He woke to the sound of Jack's voice outside the door.

Sighing, he slowly got up to see what was going on. He opened the door and caught Jack in mid-sentence.

"Oh, hey Doctor!" Jack greeted him, smiling. "I was just telling Clara that it might be nice for you and I to hang out. Like a guy's night out. But, you know, on the TARDIS."

The Doctor blinked, surprised at the request. He was feeling slightly better, and Narang _had_ suggested that he talk to a trusted friend about some of the things they discussed, perhaps it would be a good idea to go out with Jack for a while. 

His stomach growled as he came to the end of that train of thought. He hadn't eaten since the morning.

"Only if we can get food, and I can stay in my pajamas," he answered. They were his most comfortable set, and one of the only sets of clothes he had that fit decently.

Jack shrugged.

"Sure. Want to go now?"

The Doctor looked at Clara, who was watching the interaction. 

"Go have fun," she urged. "I'll be here if you need me. Ianto and I are going to have a wine and movie night."

"If you're sure." 

She leaned in and surprised him with a quick kiss on the cheek, making him smile.

"I'm sure. Go enjoy."

00

"You sure you don't want some?" The Doctor asked, motioning towards the massive plate of cheese fries that he was currently demolishing. He was on his second portion. He really had been starving.

"I don't want to lose a hand if I try to take one," Jack joked.

They were sitting in a bar in the TARDIS. The Doctor hadn't been there in forever, but it did have good food and drinks from all over the universe. Jack sipped a cocktail while the Doctor drank one of the most sugary things that Jack had ever seen. It included three types of juice and something like fifteen spoonfuls of sugar, topped with a handful of maraschino cherries.

The Doctor didn't acknowledge his statement, instead he shoved another three fries in his mouth.

"So how was it today? If you want to tell me," Jack said, after a brief silence. 

The Doctor stopped eating.

"It was... difficult. I'm still not really sure what to make of it. I still have so many questions. And she said I should talk to someone about it all, a friend perhaps." He looked at Jack.

"Hey, I'm happy to discuss anything you like. You've seemed really upset lately, is it anything I can help with?"

The Doctor frowned.

"She said... she said I should tell you what happened. But I don't know that I can say it. Perhaps I can show you."

"If you'd like."

"I'm afraid you'll think less of me, though," the Doctor admitted.

"You know I won't. We went through that year on the Valiant together, Doctor. We were tortured together. We have so much history. I'll never think less of you."

The Doctor nodded. Deep inside, he knew that Jack was telling the truth.

"I can send it telepathically... but it's bad, Jack. It's really bad."

"Okay. I'll brace myself."

The Doctor moved their plates and drinks out of the way and placed his fingers on Jack's temples. Closing his eyes, he projected his memories into Jack's mind.

Jack saw and felt it all. It was done in a flash, but it felt like hours to him. He could feel and see everything from the Doctor's perspective, from his fear when he was first handcuffed, to the nausea he felt as Missy sucked him off. He could feel the chafing of the metal against the Doctor's wrists and the burning and tearing in his backside as Missy pushed yet another sex toy inside him.

Jack was crying by the time the Doctor released him. Without a word, he pushed away from the table and ran to the bathroom, punching a wall when got inside.

00

The Doctor was near hyperventilating when he returned, and Jack instantly felt guilty.

"You're back," the Doctor said, trying to force himself to calm down. "I'm s-sorry."

Jack took his hands.

"Don't be. I'm so sorry I ran off. Just, seeing what happened to you... feeling it... God, Doctor. I want to kill her."

"It made me dirty," the Doctor mumbled.

Jack was still holding his hands, and he felt the Doctor start to shake.

"Dirty?"

"Used. Unworthy."

Jack closed his eyes, trying to push down the rage that was building inside of him. Whenever he met with Missy, he would fucking destroy her.

Taking a deep breath to calm himself, he finally replied.

"You're not. You're not dirty, or unworthy, nothing like that. You're wonderful, Doctor. I think so, Clara definitely thinks so... she loves you so much, you know."

The Doctor paled at the mention of Clara's name.

"That's the other thing. I'm so scared to lose her."

With that, the dam broke and he began to tear up. He tried to remember his anxiety exercises, but found he couldn't bring himself to try them. 

"Oh, hey, okay," Jack said, his tone softening. He moved to the other side of the booth and sat down next to the Doctor.

"Hug?" He offered.

The Doctor nodded and wrapped his arms around Jack, who held him and silently rubbed his back. 

The sobs caused him to hiccup and suddenly he began to feel sick. The combination of a huge meal and hysteria wasn't agreeing with him.

"You're going to make yourself sick," Jack said. "You need to try to calm down. I'm sure Clara's not going to leave you, okay? Please take a breath, Doctor."

Jack's words calmed him slightly.

"W-why do you think?" He said, before hiccuping again. He covered his mouth and forced himself to breath through his nose.

"Because she loves you so much. And people like her don't give up on those they love. Now come on, breath with me. In and out."

The Doctor followed Jack's lead until the nausea finally tapered off. He said back and rubbed his stomach, feeling very drained.

"Why don't we go to the library and talk some more there," Jack suggested. There were couches there and it was way more comfortable.

The Doctor nodded in agreement and allowed Jack to help him to his feet.

00

The Doctor lay on the couch, his head resting on a pillow on Jack's lap. Jack had pulled a throw blanket over him. He found the Doctor kind of adorable like this, but he didn't voice that thought.

"You said you had questions," Jack said.

"She... Narang... told me that you might be able to answer some questions. Because you're more experienced."

"I take it you mean sexually experienced?"

"Yes."

"Alright. Go on."

"Do you ever masturbate?"

Jack raised an eyebrow. 

"Well, sometimes. To be frank, Ianto and I have an active sex life, so I don't really need to, but yes, on occasion."

"I can't even do that. I didn't do it before. Not in this body. A little in the last one, but not often. I think of Clara, and how beautiful she is, and I want to. But then when it starts, my mind goes to Missy, and what she did. So you see the issue."

Jack frowned.

"Yeah. If you can't even touch yourself, how can you be intimate with Clara."

"Exactly."

"Well, personally, I think it's something you need to try to take back control over. You have to remember, that's _your_ time. You can think about whoever you want, doing whatever you want them to do. Missy has no place there. Every time she comes to mind during that, try to force her away. It might take time, so you should start slow. If she comes to mind, stop, and tell yourself she isn't there, she can't hurt you now. And try to start back up."

"Narang suggested something similar," the Doctor noted. 

"I'm being completely honest when I say this, I think Clara will wait however long it takes for you to be okay with intimacy. You need to tell her about this though. Let her know what's happening, otherwise she will just think you're pulling away."

"I know," the Doctor sighed. "It's just so embarrassing. On Gallifrey, we didn't do such things. I mean, we did, but not often, it wasn't something particularly acceptable, so we're quite repressed to an extent. It's hard to get the words out to her."

"Then maybe consider writing it down? Or using your telepathy to get the message across?"

The idea of sending that type of message to Clara's mind made the Doctor cringe.

"Perhaps writing it is a good idea. Narang said I ought to keep a journal of my thoughts anyway."

"Yeah. That's smart. And Clara is really accepting and loving. She'll understand."

Now that he was calmer, and talking things through, the Doctor realized that Jack was probably right.


	19. Chapter 19

Narang and Jack had suggested exploring his own body before anything, so that was what the Doctor was currently doing. Locked in his bedroom, he stood naked in front of a mirror, looking himself over.

The sight wasn't a particularly nice one. He knew that he had changed appearance wise, but now he was seeing every detail of it. His stomach stuck out as if he'd swallowed a ball, and his skin was lined with angry red marks. The small amount of hair that had been on his chest had faded, and his nipples had gotten darker. He touched one gently, shuddering at the sensation. He was so much more sensitive now. 

How he wished he was in one of his younger bodies. Had this happened one or two regenerations ago, he wouldn't have looked nearly so bad. Sure, he wouldn't have looked great, but now he just looked awkward. 

And it would only get worse from here. 

The thought made him even more depressed. He was just over halfway through this. If he looked bad now, what about in another five months?

Maybe it was best just to forget about this whole thing with Clara until after the baby was born. Assuming his body even went back to normal after that.

Yet she still seemed to like him. Just that morning she had said that he looked handsome. He didn't understand it. 

He shook his head and began to put his clothes back on - another set of pajamas. They fit him best these days. How Clara could ever find him attractive when he wasn't even wearing "real" clothes was beyond him.

00

Clara worried about the Doctor. Granted, she always worried about him, but he had been doing so well and lately it seemed as if he was nervous or distracted. He seemed to both want to avoid contact with her and to need it. He wouldn't meet her gaze, but would ask to cuddle with her in her room for the night.

The weird thing was, as time went on, she swore she could feel his feelings. When he'd come down to dinner dressed in his pajamas, she felt a wave of insecurity and worry coming from him. It wasn't as if she could feel everything, but like an echo of his emotions.

She decided to bring it up after their meal. She sat down across from the Doctor and watched as he served himself a large bowl of the pasta she'd made.

"Are Jack and Ianto joining us?" He asked.

"No, they ate earlier."

He nodded in acknowledgement and quietly began to eat his food. He was hungry, but made an attempt to eat slowly as to be polite to Clara. He was on his third bite when he felt something. He put his fork down and tried to concentrate on it.

"You alright?" Clara asked.

"Er, yeah. Just, I can understand her? Sort of."

"The baby?" 

"I can understand that she is hungry. And likes the pasta. Or the nutrients from the pasta. Makes sense, Time Lords are touch telepaths, so I'm feeling her thoughts. No words yet, she can't speak, obviously. She's grown just enough to project to me."

"Wow. That's... amazing, Doctor. And oddly close to the same subject I was going to bring up with you."

"You can feel my emotions, right?" He asked.

"Yeah. You knew?"

"I could sense it, sort of. It means I've formed a bond with you."

"And what does that mean? Are we married or something?"

The Doctor couldn't help but smile at the question.

"It happens if a Time Lord becomes very close with another being. Usually it only happens with other Time Lords. Missy and I had one when we were young, but it was broken. It can happen on purpose or naturally. This one seems to be natural. My telepathic reach has increased as the baby's abilities have grown, and it's reached you, too. But you wouldn't be able to pick up on it unless we were close and had a trust between us. Not in the way you're picking it up."

"So Jack and Ianto can't feel this?"

"Jack might be able to feel it slightly, because we've known each other so long, but you're most attuned to it because of the time we have spent together. I hope it's okay?"

She felt a pang of nervousness come over her. It was coming from the Doctor.

"Yes, of course it's okay. It's an honor, really."

Then a small sense of relief.

"Maybe it'll help me to help you," she added. "If I can feel your emotions, then you can feel mine?"

"If you focus them at me, but it might be hard. Humans are not natural telepaths."

Clara nodded and closed her eyes. A second later, the Doctor felt an amazing sense of warmth and calm. The only way he could describe it was as if someone were holding him, the way Clara often did at night.

"That's from you?" He asked.

"Mhm. Just so you know how much I care about you."

The Doctor felt a little happier after that.


	20. Chapter 20

It took another month and a half for Jack and Ianto to finish their trap. Just in time, too, because the TARDIS was giving more and more alerts that they were being tracked. In fact, the last time they'd touched down on another planet, there was an alert that someone or something was incoming towards them. They managed to get away just in time it seemed.

After discussing it with Clara, Jack and Ianto decided it was best to tell the Doctor what was going on the day that they tested their invention. Clearly their time was running out, Missy would find them sooner rather than later and they couldn't just stay in the vortex forever.

Clara could feel the Doctor's nervousness as he walked into the library, their designated meeting space. She motioned for him to sit next to her on the couch and started trying to calm him, but he resisted her.

"Just tell me what's going on," he said, in a frustrated tone. 

"Missy's looking for us," Jack answered. Might as well get right to the point.

"You mean she's looking for _me_." 

Clara could feel his anxiety heighten, along with a sense of anger and pain.

"Yes. But we're all here, so we'll help protect you. And on that end -"

"How long? How long has she been searching?"

Jack looked at Clara, who frowned.

"A few months. Since after you left the hospital."

"The TARDIS didn't alert me."

His words were calm, almost too calm, and it put Clara on edge.

"She alerted me. I think she didn't want to stress you any more than you already were."

"So you kept this from me then."

"Well, yes, but honestly it was out of necessity. You were so upset and having so many issues, to add this on top of it..." she trailed off.

The Doctor opened his mouth to speak, but Jack beat him to it.

"The important thing is that we have a plan. Ianto and I have been working on it for some time, and we really think it'll work, and it will meet everyone's criteria for what to do with her."

The Doctor stared at him.

"I'm listening."

Clara could feel that he was still angry, but was pushing it down, for now at least.

Jack held up the electrode, which was circular and about the size of a half dollar. 

"It's using a bit of more advanced tech, but basically, this will stick on whoever we throw it at. It's remotely connected to this," he held up a small remote, "and once the button is hit, it will release three wires that will go for her weakest points. Another push and she gets hit with 500 volts. Enough to stun her, we think. You guys are tougher than humans, so we're kind of guessing here. When she's stunned, we use these," Jack held up a pair of rubber gloves, "to attach a one-trip vortex manipulator. She gets sent to the newest holding cell at Torchwood and the manipulator self destructs. The holding cell will fill with a liquid that should keep her in stasis."

"That's pretty smart. It should work," the Doctor admitted.

"We just have to test it," Jack said.

"And that's why you're telling me this now," the Doctor concluded.

"Yeah. I was thinking it can be tested on me, since I can't die. Not long term anyway."

"Alright. What about the vortex manipulator? They're pretty rare."

"Once you know how they work they aren't all that hard to create, especially not one use ones. We made three."

"You really thought of everything." The Doctor seemed calmer now, which made Clara feel a little better.

"We tried. You're very important to us, Doc."

The Doctor half smiled.

"I'm grateful to you. So, do you want to test it now?"

00

Jack stood in one of the hallways and forced himself to relax. The plan was simple. Ianto would throw the electrode at him and place the vortex manipulator on his wrist. Once he was gone, the Doctor would bring the TARDIS to the location where Jack was being held.

"See you soon," Ianto said. With that he threw the gadget and pressed a button on his remote. It landed on Jack's shirt. What looked like 3 black wires grew from it. Two attached to his heart and one to his brainstem. He began to shake as the voltage flowed through his body. 

Ianto calmly stepped forward, donning a pair of forearm length gloves that allowed him to bypass the electricity. He grabbed Jack's shaking arm and placed the vortex manipulator on it then pressed a button. In a second, Jack was gone.

00

They arrived at the Torchwood base seconds after Jack did. He was already in the holding cell. Ianto tapped another button and the electrode fell off of Jack's body.

"Good Lord," Jack said, after a minute for recovery. "That hurt like hell."

"It worked, too. Once she's here we can fill the cell with stasis fluid. It'll keep her there for as long as we want."

With that, Ianto typed in a long and complex code into a box near the cell door and allowed it to scan his retina. Only then did the door open, allowing Jack to walk out.

00

Clara found that if she concentrated, she could narrow down the Doctor's feelings. Instead of just feeling general anxiety, she would get a gist as to what was causing it, usually by seeing quick pictures in her mind. She told the Doctor about it immediately- being able to sense his thoughts and keeping it secret seemed like a massive betrayal, but he was surprisingly okay with it.

It was hard for him to get the right words out sometimes and she felt a sense of relief from him. If he couldn't explain things, she would still understand. And of course if he really wanted to, he could block her out.

That night as they lay together in bed she sensed many feelings coming from him. One was gratitude, both towards her and towards Jack and Ianto, but the other big one was fear. He was nervous again. She closed her eyes and saw images of Missy, of handcuffs and of a small, premature baby. 

Frowning, she wrapped an arm around him and rested her face on his chest. She did her best to send him loving, calm thoughts and mental pictures of her, Jack and Ianto protecting him. It drained her to do it for more than a few minutes, but she decided it was worth the tiredness when she felt his fear recede as he finally fell asleep.


	21. Chapter 21

**Notes for the Chapter:**

> I'm committed to finishing this. Better late than never.

Things began to once again get better as the Doctor approached his eighth month of pregnancy. They’d been in the vortex, avoiding Missy, and though he knew it wasn’t a permanent solution, his anxiety had lessened somewhat.

His relationship with Clara had also progressed to a more intimate level. 

Of course, it had started off slowly. There was more kissing and heavy petting, mostly on the Doctor’s part. He felt most comfortable when allowed to remain in control, so he’d been slowly becoming accustomed to touching Clara’s body. He would rest his hand on her side, or gently cup her breast. Over time, there were less clothes. They’d kiss wearing only their pants; Clara in her bra and the Doctor shirtless. 

While he still felt anxiety with sexual touch, Clara would sometimes rub his belly or massage his back if he was in pain, and he liked the feeling of her hands on his skin. She was so warm and soft, and it felt amazing against him. 

It was closer than he’d allowed anyone to get to him in centuries. The bond they shared helped calm his insecurities as well; he could feel that Clara really did find him attractive, even though he viewed himself as far too fat and awkward looking.

One day, as Clara massaged a beautifully scented lotion into the Doctor’s belly, he felt her press her lips to his side. 

She looked up at him, eyes huge.

“Is that alright?” She whispered.

And he could feel something tugging at him: the feeling of lust.

In times of intense emotion, the bond sometimes felt stronger, and right then he could almost feel her frustration she felt as she got wetter and wetter. 

“Yes,” he finally answered, as he took in the feeling. He’d felt it before, but now it was absolutely radiating off of her. And suddenly, it was as if the only thing he wanted was to pleasure her.

“May I…?” He motioned at her skirt, and smiled as she nodded, stood and shimmied out of it. 

The Doctor looked her over, dressed in a bra and little lacy red panties. Stunningly gorgeous, and only wanting him.

“Lay back,” he whispered, watching as she followed his instructions. 

He moved from his perch on the side of the bed and kneeled in front of her as best he could. With shaky hands he reached to her hips, his fingers grasping the sides of her underwear and lowering it, discarding it on the floor. 

He pushed her legs farther apart and leaned in, his tongue taking her all in. She let out a moan and a wave of arousal shot through him, a mixture of his and hers. Using a combination of instinct and the bond, he managed to make her writhe and finish shortly thereafter. 

Things shifted after that. It was almost as if his actions had opened a floodgate and he was becoming more willing to try new things. Going fully all the way still scared him, but he at least felt like he might actually get there one day, instead of being stuck in a non-intimate relationship forever.

00

To avoid the possibility of Missy finding him as he gave birth, the Doctor began conversing with the doctors on Therilian about potentially bringing them into the TARDIS instead of him going to their office. His ship could easily provide the tools, room and any medication they might need, and he would of course compensate them generously for their trouble. When they finally agreed, he felt calmer than he had in months, and for once, slept through the entire night with no nightmares.

Two weeks later, he woke up in pain.

00

The pain started out more as discomfort. The Doctor felt he had perhaps pulled a muscle in his back, but as the day progressed the pain grew worse and worse, coming in waves.

Everyone else was extremely concerned. The Doctor was too, but he didn’t want to leave the vortex unnecessarily. A video conference with his healers was held, and while they thought he may be experiencing false contractions, they wanted him to come in.

He wanted a second opinion. He ordered Clara to scan him in the med-bay, and was part way through that when he began to bleed. 

Clara immediately dropped the scanner.

“We need to go,” she said, trying to keep as calm as possible, knowing he could sense her panic and that it would only make him feel worse.

He said nothing, but his heart rates began to increase. 

“We’re going to get Jack and Ianto, and we’re going to go see the healers, alright?” She said, squeezing his hand. “You just wait here.”

The Doctor nodded and took a deep breath. This was bad, very bad. Not only was he risking being found by his rapist, but his child could be in danger. 

The thoughts were too much. He felt more blood dripping down his leg and he began to breathe harder, panting as he started to hyperventilate. 

Soon he began to feel dizzy. Whether it was from blood loss or panic he wasn’t sure. He forced himself to sit back on the examination bed, just making it before everything went black.


	22. Chapter 22

The Doctor woke up in a Therilian hospital room. There were lines connected to his arm, dripping medicines into him, and Clara was at his side.

“Hey you,” she said, smiling at him. He weakly reached for her hand, wanting the comfort of her touch.

“What happened?” He asked, his voice hoarse. “Is… is she alright?”

The heart rate monitor began to spike again, and Clara quickly nodded ‘yes’. 

“Doctor, you need to calm down. You’re alright, the baby is fine. The placenta thinned out a lot and wasn’t attached to your uterus entirely, which caused the bleeding. But they stopped it, and checked the baby, and you’re both alright. Now take a deep breath.”

The Doctor did as he was instructed, feeling better already. 

“Now, you’ll have to stay overnight. I know you don’t want to, but the medication they’re giving to help you is slow acting and they want to watch you. Jack and Ianto are right outside the door keeping watch. I’ll be with you the whole time.”

And just like that, the fear returned.

“I’d rather go,” the Doctor whispered, feeling himself tear up. “Can’t we please go?”

“I’d rather leave too but the healers assured me that it’s best for you and your daughter, Doctor.” She squeezed his hand and kissed it. “We won’t let her get you.”

The Doctor shook his head sadly.

“You can’t promise that.”

00

The evening passed quietly. Clara tried to distract the Doctor by talking about baby names and plans for the nursery, while Jack and Ianto continued to stand guard, but the Doctor couldn’t relax. Missy was coming, he just knew it. He could feel it. And he’d be helpless against her.

He’d finally managed to drift off to sleep in the early morning hours. And of course, that was when the shouting started. 

It began in the offices down the hall, as Missy worked her way through, injuring or killing the healers in her way. She grabbed one - a small, mousy looking healer who seemed easy enough to drag along - and forced her down the halls as she began checking the rooms for her target. 

The Doctor heard the screams first. He woke to find Clara standing next to him, a weapon in hand.

“You stay put. We’ve got this,” she told him, a determined expression on her face.

“No! No, we need to leave,” the Doctor said, “Please, Clara. Let’s go!”

He was cut off by the sound of Jack’s voice.

“You’re not getting in there,” he growled, blocking the door with his body. 

Ianto began readying the electrodes and was about to throw them when Missy shoved the healer in his direction, knocking him off balance. As he moved to recover, she quickly shot Jack and worked her way inside the room. She’d just nearly made it to the Doctor when Ianto reappeared, nearly tripping over himself as he threw the electrodes at her. She looked stunned as he pressed the button that set them off and fell to the floor, shaking and seizing as the current moved through her.

Ianto threw the vortex manipulator at Clara, who was closest to Missy.

“Put it on her, use these!” he threw a pair of gloves at her. 

Quickly as possible, Clara put on the gloves and tried to take hold of Missy’s arm. Despite the power of the current pushing through her, Missy was clearly trying to fight back. Clara had just gotten the manipulator on her when Missy surprised her by reaching up. Just as Clara pushed the button, Missy took hold of the Doctor’s hand, and both of them disappeared.

00

“Shit,” Jack cursed, as he made his way into the room. He turned to Clara, who was already pushing past him to get to the TARDIS.

“Do you know how to fly it?” Jack asked, as he and Ianto followed behind.

“Of course not.” She threw open the door and walked in. “But maybe… maybe we can use the telepathic circuits. Here,” she led Jack over to where gel was kept. “Put your hands in, picture Torchwood, and the TARDIS should be able to take us."

Jack rolled up his sleeves and did as he was told, grimacing at how cool and gross the gel felt against his skin. He closed his eyes and pictured the specific cell in the Torchwood basement where they’d intended Missy to be kept. Within seconds the TARDIS started up.

00

Upon landing the three immediately raced from the box. The cell was directly in front of them, but Missy wasn’t in it. Instead they saw the Doctor, chained by his wrists to the wall as the stasis fluid filled the space. It was up to his knees. He was shaking, had his eyes closed and looked to be in great pain, but wasn’t making any sounds.

“Get him out,” Clara said frantically. 

Ianto moved to unlock the cell while Jack looked for Missy. She had to be somewhere, there hadn’t been enough time for her to leave, unless she had a vortex manipulator of her own.

It was a sound that gave her away. Jack turned just in time to see her raise a gun to his head. The gunshot went off just as Ianto released the Doctor from his chains, the sound causing the Doctor to cringe. He fell as he was released, Ianto just managing to catch him. Clara was instantly at his side. 

“Is all of this _really_ the best you can do?” Missy asked, as she strolled towards them. “I expected better.”

“Get. Away,” Clara growled, positioning herself between Missy and the Doctor.

Ianto took that as his cue to get the Doctor farther away and managed to drag him to the corner of the room, standing in front of him as well. Still, Missy stalked closer to them. 

“Why don’t we just make this easy? Hand him over. It’s not as if I plan to kill him, anyway,” she grinned. 

Clara and Ianto stood their ground, staring her directly in the face.

“You’ll get to him over my dead body,” Clara replied. 

Missy shrugged. 

“That’s fine, then.” She was about five feet away. Clara wasn’t armed, but she would do her damndest to protect her lover. 

Missy took another step, then stopped as a flash appeared between her and Clara. Suddenly, Jack was standing there. Without a second’s hesitation, stabbed her, hitting Missy directly in one of her hearts.

Missy’s eyes widened, stunned at what had happened. It wasn’t a fatal wound, but -

Jack twisted the dagger and pushed Missy back towards the cell. With all of his might he shoved her inside and hit the button to close it off. Within seconds the room began to fill. Missy, with only one heart still working, was too weak to do anything more than stare at them as fluid slowly took hold. 

"Good thing we built a few of those," Jack said, tapping the vortex manipulator on his wrist.


End file.
